diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1521ee378738..a696213d4770 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ### Features
 
+- `[jest-config]` [**BREAKING**] Move coverage options to project config ([#9633](https://github.com/facebook/jest/pull/9633))
 - `[jest-runtime]` Require stack when a module cannot be resolved ([#9681](https://github.com/facebook/jest/pull/9681))
 - `[jest-config]` Support ESM config files with `.js` extension ([#9573](https://github.com/facebook/jest/pull/9573)).
 - `[jest-runtime]` Override `module.createRequire` to return a Jest-compatible `require` function ([#9469](https://github.com/facebook/jest/pull/9469))
diff --git a/TestUtils.ts b/TestUtils.ts
index a84f3f8bc630..407f18f79f86 100644
--- a/TestUtils.ts
+++ b/TestUtils.ts
@@ -12,12 +12,9 @@ const DEFAULT_GLOBAL_CONFIG: Config.GlobalConfig = {
   changedFilesWithAncestor: false,
   changedSince: '',
   collectCoverage: false,
-  collectCoverageFrom: [],
-  collectCoverageOnlyFrom: null,
   coverageDirectory: 'coverage',
   coverageProvider: 'babel',
   coverageReporters: [],
-  coverageThreshold: {global: {}},
   detectLeaks: false,
   detectOpenHandles: false,
   enabledTestsMap: null,
@@ -71,7 +68,10 @@ const DEFAULT_PROJECT_CONFIG: Config.ProjectConfig = {
   cache: false,
   cacheDirectory: '/test_cache_dir/',
   clearMocks: false,
+  collectCoverageFrom: [],
+  collectCoverageOnlyFrom: null,
   coveragePathIgnorePatterns: [],
+  coverageThreshold: {global: {}},
   cwd: '/test_root_dir/',
   detectLeaks: false,
   detectOpenHandles: false,
diff --git a/docs/WatchPlugins.md b/docs/WatchPlugins.md
index 3f99779ed3fa..7fd26d1d4da9 100644
--- a/docs/WatchPlugins.md
+++ b/docs/WatchPlugins.md
@@ -157,8 +157,6 @@ For stability and safety reasons, only part of the global configuration keys can
 - [`bail`](configuration.html#bail-number--boolean)
 - [`changedSince`](cli.html#--changedsince)
 - [`collectCoverage`](configuration.html#collectcoverage-boolean)
-- [`collectCoverageFrom`](configuration.html#collectcoveragefrom-array)
-- [`collectCoverageOnlyFrom`](configuration.html#collectcoverageonlyfrom-array)
 - [`coverageDirectory`](configuration.html#coveragedirectory-string)
 - [`coverageReporters`](configuration.html#coveragereporters-arraystring)
 - [`notify`](configuration.html#notify-boolean)
diff --git a/e2e/__tests__/__snapshots__/showConfig.test.ts.snap b/e2e/__tests__/__snapshots__/showConfig.test.ts.snap
index 7f3d73efee7c..0c5a4c6aa043 100644
--- a/e2e/__tests__/__snapshots__/showConfig.test.ts.snap
+++ b/e2e/__tests__/__snapshots__/showConfig.test.ts.snap
@@ -9,6 +9,7 @@ exports[`--showConfig outputs config info and exits 1`] = `
       "cache": false,
       "cacheDirectory": "/tmp/jest",
       "clearMocks": false,
+      "collectCoverageFrom": [],
       "coveragePathIgnorePatterns": [
         "/node_modules/"
       ],
@@ -82,7 +83,6 @@ exports[`--showConfig outputs config info and exits 1`] = `
     "bail": 0,
     "changedFilesWithAncestor": false,
     "collectCoverage": false,
-    "collectCoverageFrom": [],
     "coverageDirectory": "<<REPLACED_ROOT_DIR>>/coverage",
     "coverageProvider": "babel",
     "coverageReporters": [
diff --git a/packages/jest-config/src/index.ts b/packages/jest-config/src/index.ts
index 85b6e34546d8..d2dc49d1140c 100644
--- a/packages/jest-config/src/index.ts
+++ b/packages/jest-config/src/index.ts
@@ -109,12 +109,9 @@ const groupOptions = (
     changedFilesWithAncestor: options.changedFilesWithAncestor,
     changedSince: options.changedSince,
     collectCoverage: options.collectCoverage,
-    collectCoverageFrom: options.collectCoverageFrom,
-    collectCoverageOnlyFrom: options.collectCoverageOnlyFrom,
     coverageDirectory: options.coverageDirectory,
     coverageProvider: options.coverageProvider,
     coverageReporters: options.coverageReporters,
-    coverageThreshold: options.coverageThreshold,
     detectLeaks: options.detectLeaks,
     detectOpenHandles: options.detectOpenHandles,
     enabledTestsMap: options.enabledTestsMap,
@@ -167,7 +164,10 @@ const groupOptions = (
     cache: options.cache,
     cacheDirectory: options.cacheDirectory,
     clearMocks: options.clearMocks,
+    collectCoverageFrom: options.collectCoverageFrom,
+    collectCoverageOnlyFrom: options.collectCoverageOnlyFrom,
     coveragePathIgnorePatterns: options.coveragePathIgnorePatterns,
+    coverageThreshold: options.coverageThreshold,
     cwd: options.cwd,
     dependencyExtractor: options.dependencyExtractor,
     detectLeaks: options.detectLeaks,
diff --git a/packages/jest-core/src/__tests__/watch.test.js b/packages/jest-core/src/__tests__/watch.test.js
index af2dea274d7a..43653a5d77aa 100644
--- a/packages/jest-core/src/__tests__/watch.test.js
+++ b/packages/jest-core/src/__tests__/watch.test.js
@@ -600,11 +600,8 @@ describe('Watch mode flows', () => {
     ${'✖︎'} | ${'changedFilesWithAncestor'}
     ${'✔︎'} | ${'changedSince'}
     ${'✔︎'} | ${'collectCoverage'}
-    ${'✔︎'} | ${'collectCoverageFrom'}
-    ${'✔︎'} | ${'collectCoverageOnlyFrom'}
     ${'✔︎'} | ${'coverageDirectory'}
     ${'✔︎'} | ${'coverageReporters'}
-    ${'✖︎'} | ${'coverageThreshold'}
     ${'✖︎'} | ${'detectLeaks'}
     ${'✖︎'} | ${'detectOpenHandles'}
     ${'✖︎'} | ${'enabledTestsMap'}
diff --git a/packages/jest-core/src/lib/__tests__/__snapshots__/log_debug_messages.test.ts.snap b/packages/jest-core/src/lib/__tests__/__snapshots__/log_debug_messages.test.ts.snap
index 3be6c4ebb716..3148b01fb27a 100644
--- a/packages/jest-core/src/lib/__tests__/__snapshots__/log_debug_messages.test.ts.snap
+++ b/packages/jest-core/src/lib/__tests__/__snapshots__/log_debug_messages.test.ts.snap
@@ -8,7 +8,12 @@ exports[`prints the config object 1`] = `
     "cache": false,
     "cacheDirectory": "/test_cache_dir/",
     "clearMocks": false,
+    "collectCoverageFrom": [],
+    "collectCoverageOnlyFrom": null,
     "coveragePathIgnorePatterns": [],
+    "coverageThreshold": {
+      "global": {}
+    },
     "cwd": "/test_root_dir/",
     "detectLeaks": false,
     "detectOpenHandles": false,
@@ -68,14 +73,9 @@ exports[`prints the config object 1`] = `
     "changedFilesWithAncestor": false,
     "changedSince": "",
     "collectCoverage": false,
-    "collectCoverageFrom": [],
-    "collectCoverageOnlyFrom": null,
     "coverageDirectory": "coverage",
     "coverageProvider": "babel",
     "coverageReporters": [],
-    "coverageThreshold": {
-      "global": {}
-    },
     "detectLeaks": false,
     "detectOpenHandles": false,
     "enabledTestsMap": null,
diff --git a/packages/jest-core/src/lib/update_global_config.ts b/packages/jest-core/src/lib/update_global_config.ts
index 992a03631bdd..f3260ebdf393 100644
--- a/packages/jest-core/src/lib/update_global_config.ts
+++ b/packages/jest-core/src/lib/update_global_config.ts
@@ -56,14 +56,6 @@ export default (
     newConfig.collectCoverage = options.collectCoverage || false;
   }
 
-  if (options.collectCoverageFrom !== undefined) {
-    newConfig.collectCoverageFrom = options.collectCoverageFrom;
-  }
-
-  if (options.collectCoverageOnlyFrom !== undefined) {
-    newConfig.collectCoverageOnlyFrom = options.collectCoverageOnlyFrom;
-  }
-
   if (options.coverageDirectory !== undefined) {
     newConfig.coverageDirectory = options.coverageDirectory;
   }
diff --git a/packages/jest-core/src/watch.ts b/packages/jest-core/src/watch.ts
index 49c74bf981bc..0fa4f60b73e5 100644
--- a/packages/jest-core/src/watch.ts
+++ b/packages/jest-core/src/watch.ts
@@ -103,8 +103,6 @@ export default function watch(
     bail,
     changedSince,
     collectCoverage,
-    collectCoverageFrom,
-    collectCoverageOnlyFrom,
     coverageDirectory,
     coverageReporters,
     mode,
@@ -122,8 +120,6 @@ export default function watch(
       bail,
       changedSince,
       collectCoverage,
-      collectCoverageFrom,
-      collectCoverageOnlyFrom,
       coverageDirectory,
       coverageReporters,
       mode,
diff --git a/packages/jest-reporters/src/__tests__/coverage_reporter.test.js b/packages/jest-reporters/src/__tests__/coverage_reporter.test.js
index 7e1cf5c4ceb6..10d5058918b7 100644
--- a/packages/jest-reporters/src/__tests__/coverage_reporter.test.js
+++ b/packages/jest-reporters/src/__tests__/coverage_reporter.test.js
@@ -133,19 +133,23 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           global: {
             statements: 100,
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(1);
       });
@@ -167,15 +171,19 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
-        coverageThreshold: covThreshold,
       },
       {
         maxWorkers: 2,
       },
     );
+    const context = {
+      config: {
+        coverageThreshold: covThreshold,
+      },
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(5);
       });
@@ -197,15 +205,19 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
-        coverageThreshold: covThreshold,
       },
       {
         maxWorkers: 2,
       },
     );
+    const context = {
+      config: {
+        coverageThreshold: covThreshold,
+      },
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError()).toBeUndefined();
       });
@@ -215,19 +227,23 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           'path-test-files/non_covered_file.js': {
             statements: 100,
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(1);
       });
@@ -237,19 +253,23 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path-test-files/glob-path/': {
             statements: 100,
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(1);
       });
@@ -259,19 +279,23 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path-test-files/glob-path/': {
             statements: 40,
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError()).toBeUndefined();
       });
@@ -281,19 +305,23 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path/doesnt/exist': {
             statements: 40,
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(1);
       });
@@ -305,6 +333,13 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path-test-files/': {
             statements: 50,
@@ -314,13 +349,10 @@ describe('onRunComplete', () => {
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError()).toBeUndefined();
       });
@@ -346,15 +378,19 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
-        coverageThreshold: covThreshold,
       },
       {
         maxWorkers: 2,
       },
     );
+    const context = {
+      config: {
+        coverageThreshold: covThreshold,
+      },
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError()).toBeUndefined();
       });
@@ -366,6 +402,13 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path-test-files/100pc_coverage_file.js': {
             statements: 100,
@@ -375,15 +418,12 @@ describe('onRunComplete', () => {
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     // 100% coverage file is removed from overall coverage so
     // coverage drops to < 50%
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError().message.split('\n')).toHaveLength(1);
       });
@@ -393,6 +433,13 @@ describe('onRunComplete', () => {
     const testReporter = new CoverageReporter(
       {
         collectCoverage: true,
+      },
+      {
+        maxWorkers: 2,
+      },
+    );
+    const context = {
+      config: {
         coverageThreshold: {
           './path-test-files/': {
             statements: 50,
@@ -408,13 +455,10 @@ describe('onRunComplete', () => {
           },
         },
       },
-      {
-        maxWorkers: 2,
-      },
-    );
+    };
     testReporter.log = jest.fn();
     return testReporter
-      .onRunComplete(new Set(), {}, mockAggResults)
+      .onRunComplete(new Set([context]), {}, mockAggResults)
       .then(() => {
         expect(testReporter.getLastError()).toBeUndefined();
       });
diff --git a/packages/jest-reporters/src/__tests__/get_watermarks.test.ts b/packages/jest-reporters/src/__tests__/get_watermarks.test.ts
index 2b47c5159e09..d559c58b5d12 100644
--- a/packages/jest-reporters/src/__tests__/get_watermarks.test.ts
+++ b/packages/jest-reporters/src/__tests__/get_watermarks.test.ts
@@ -6,39 +6,70 @@
  */
 
 import getWatermarks from '../get_watermarks';
-import {makeGlobalConfig} from '../../../../TestUtils';
+import {makeProjectConfig} from '../../../../TestUtils';
 
 describe('getWatermarks', () => {
-  test(`that watermarks use thresholds as upper target`, () => {
-    const watermarks = getWatermarks(
-      makeGlobalConfig({
-        coverageThreshold: {
-          global: {
-            branches: 100,
-            functions: 100,
-            lines: 100,
-            statements: 100,
+  describe('when a single context is given', () => {
+    test(`that watermarks use thresholds as upper target`, () => {
+      const context = {
+        config: makeProjectConfig({
+          coverageThreshold: {
+            global: {
+              branches: 100,
+              functions: 100,
+              lines: 100,
+              statements: 100,
+            },
           },
-        },
-      }),
-    );
-
-    expect(watermarks).toEqual({
-      branches: [expect.any(Number), 100],
-      functions: [expect.any(Number), 100],
-      lines: [expect.any(Number), 100],
-      statements: [expect.any(Number), 100],
+        }),
+      };
+      const watermarks = getWatermarks(new Set([context]));
+
+      expect(watermarks).toEqual({
+        branches: [expect.any(Number), 100],
+        functions: [expect.any(Number), 100],
+        lines: [expect.any(Number), 100],
+        statements: [expect.any(Number), 100],
+      });
     });
   });
 
-  test(`that watermarks are created always created`, () => {
-    const watermarks = getWatermarks(makeGlobalConfig());
+  describe('when no contexts are given', () => {
+    test(`that watermarks are created always created`, () => {
+      const watermarks = getWatermarks(new Set());
+
+      expect(watermarks).toEqual({
+        branches: [expect.any(Number), expect.any(Number)],
+        functions: [expect.any(Number), expect.any(Number)],
+        lines: [expect.any(Number), expect.any(Number)],
+        statements: [expect.any(Number), expect.any(Number)],
+      });
+    });
+  });
+
+  describe('when multiple contexts are given', () => {
+    test(`that watermarks are created always created`, () => {
+      const context = {
+        config: makeProjectConfig({
+          coverageThreshold: {
+            global: {
+              branches: 100,
+              functions: 100,
+              lines: 100,
+              statements: 100,
+            },
+          },
+        }),
+      };
+
+      const watermarks = getWatermarks(new Set([context, context]));
 
-    expect(watermarks).toEqual({
-      branches: [expect.any(Number), expect.any(Number)],
-      functions: [expect.any(Number), expect.any(Number)],
-      lines: [expect.any(Number), expect.any(Number)],
-      statements: [expect.any(Number), expect.any(Number)],
+      expect(watermarks).toEqual({
+        branches: [expect.any(Number), expect.any(Number)],
+        functions: [expect.any(Number), expect.any(Number)],
+        lines: [expect.any(Number), expect.any(Number)],
+        statements: [expect.any(Number), expect.any(Number)],
+      });
     });
   });
 });
diff --git a/packages/jest-reporters/src/coverage_reporter.ts b/packages/jest-reporters/src/coverage_reporter.ts
index b769743e2ff6..d2e27130b2e8 100644
--- a/packages/jest-reporters/src/coverage_reporter.ts
+++ b/packages/jest-reporters/src/coverage_reporter.ts
@@ -100,7 +100,7 @@ export default class CoverageReporter extends BaseReporter {
     aggregatedResults: AggregatedResult,
   ): Promise<void> {
     await this._addUntestedFiles(contexts);
-    const {map, reportContext} = await this._getCoverageResult();
+    const {map, reportContext} = await this._getCoverageResult(contexts);
 
     try {
       const coverageReporters = this._globalConfig.coverageReporters || [];
@@ -133,24 +133,17 @@ export default class CoverageReporter extends BaseReporter {
       );
     }
 
-    // @ts-ignore
-    this._checkThreshold(map);
+    this._checkThresholds(map, contexts);
   }
 
   private async _addUntestedFiles(contexts: Set<Context>): Promise<void> {
     const files: Array<{config: Config.ProjectConfig; path: string}> = [];
 
     contexts.forEach(context => {
-      const config = context.config;
-      if (
-        this._globalConfig.collectCoverageFrom &&
-        this._globalConfig.collectCoverageFrom.length
-      ) {
+      const {config} = context;
+      if (config.collectCoverageFrom && config.collectCoverageFrom.length) {
         context.hasteFS
-          .matchFilesWithGlob(
-            this._globalConfig.collectCoverageFrom,
-            config.rootDir,
-          )
+          .matchFilesWithGlob(config.collectCoverageFrom, config.rootDir)
           .forEach(filePath =>
             files.push({
               config,
@@ -253,9 +246,19 @@ export default class CoverageReporter extends BaseReporter {
     }
   }
 
-  private _checkThreshold(map: istanbulCoverage.CoverageMap) {
-    const {coverageThreshold} = this._globalConfig;
+  private _checkThresholds(
+    map: istanbulCoverage.CoverageMap,
+    contexts: Set<Context>,
+  ) {
+    contexts.forEach(context =>
+      this._checkThresholdForContext(map, context.config.coverageThreshold),
+    );
+  }
 
+  private _checkThresholdForContext(
+    map: istanbulCoverage.CoverageMap,
+    coverageThreshold?: Config.CoverageThreshold,
+  ) {
     if (coverageThreshold) {
       function check(
         name: string,
@@ -444,7 +447,9 @@ export default class CoverageReporter extends BaseReporter {
     }
   }
 
-  private async _getCoverageResult(): Promise<{
+  private async _getCoverageResult(
+    contexts: Set<Context>,
+  ): Promise<{
     map: istanbulCoverage.CoverageMap;
     reportContext: istanbulReport.Context;
   }> {
@@ -506,7 +511,7 @@ export default class CoverageReporter extends BaseReporter {
       const reportContext = istanbulReport.createContext({
         coverageMap: map,
         dir: this._globalConfig.coverageDirectory,
-        watermarks: getWatermarks(this._globalConfig),
+        watermarks: getWatermarks(contexts),
       });
 
       return {map, reportContext};
@@ -521,7 +526,7 @@ export default class CoverageReporter extends BaseReporter {
         dir: this._globalConfig.coverageDirectory,
         // @ts-ignore
         sourceFinder: this._sourceMapStore.sourceFinder,
-        watermarks: getWatermarks(this._globalConfig),
+        watermarks: getWatermarks(contexts),
       },
     );
 
diff --git a/packages/jest-reporters/src/generateEmptyCoverage.ts b/packages/jest-reporters/src/generateEmptyCoverage.ts
index 62ab4c023f2c..e84d80a10f9b 100644
--- a/packages/jest-reporters/src/generateEmptyCoverage.ts
+++ b/packages/jest-reporters/src/generateEmptyCoverage.ts
@@ -35,8 +35,6 @@ export default function (
   const coverageOptions = {
     changedFiles,
     collectCoverage: globalConfig.collectCoverage,
-    collectCoverageFrom: globalConfig.collectCoverageFrom,
-    collectCoverageOnlyFrom: globalConfig.collectCoverageOnlyFrom,
     coverageProvider: globalConfig.coverageProvider,
   };
   let coverageWorkerResult: CoverageWorkerResult | null = null;
diff --git a/packages/jest-reporters/src/get_watermarks.ts b/packages/jest-reporters/src/get_watermarks.ts
index 6c3bd174bf25..e3552d03badf 100644
--- a/packages/jest-reporters/src/get_watermarks.ts
+++ b/packages/jest-reporters/src/get_watermarks.ts
@@ -7,13 +7,19 @@
 
 import type {Config} from '@jest/types';
 import istanbulReport = require('istanbul-lib-report');
+import type {Context} from './types';
 
 export default function getWatermarks(
-  config: Config.GlobalConfig,
+  contexts: Set<Pick<Context, 'config'>>,
 ): istanbulReport.Watermarks {
   const defaultWatermarks = istanbulReport.getDefaultWatermarks();
 
-  const {coverageThreshold} = config;
+  if (contexts.size !== 1) {
+    return defaultWatermarks;
+  }
+
+  const firstAndOnlyContext = contexts.values().next().value;
+  const {coverageThreshold} = firstAndOnlyContext.config;
 
   if (!coverageThreshold || !coverageThreshold.global) {
     return defaultWatermarks;
diff --git a/packages/jest-runner/src/runTest.ts b/packages/jest-runner/src/runTest.ts
index a617bc9d510c..65d7029bbbef 100644
--- a/packages/jest-runner/src/runTest.ts
+++ b/packages/jest-runner/src/runTest.ts
@@ -156,8 +156,6 @@ async function runTestInternal(
   runtime = new Runtime(config, environment, resolver, cacheFS, {
     changedFiles: context && context.changedFiles,
     collectCoverage: globalConfig.collectCoverage,
-    collectCoverageFrom: globalConfig.collectCoverageFrom,
-    collectCoverageOnlyFrom: globalConfig.collectCoverageOnlyFrom,
     coverageProvider: globalConfig.coverageProvider,
   });
 
diff --git a/packages/jest-runtime/src/index.ts b/packages/jest-runtime/src/index.ts
index 39a43443c26c..0120bab0a2ef 100644
--- a/packages/jest-runtime/src/index.ts
+++ b/packages/jest-runtime/src/index.ts
@@ -135,8 +135,6 @@ class Runtime {
     this._coverageOptions = coverageOptions || {
       changedFiles: undefined,
       collectCoverage: false,
-      collectCoverageFrom: [],
-      collectCoverageOnlyFrom: undefined,
       coverageProvider: 'babel',
     };
     this._currentlyExecutingModulePath = '';
@@ -496,8 +494,6 @@ class Runtime {
       ...options,
       changedFiles: this._coverageOptions.changedFiles,
       collectCoverage: this._coverageOptions.collectCoverage,
-      collectCoverageFrom: this._coverageOptions.collectCoverageFrom,
-      collectCoverageOnlyFrom: this._coverageOptions.collectCoverageOnlyFrom,
       coverageProvider: this._coverageOptions.coverageProvider,
     };
   }
diff --git a/packages/jest-transform/src/__tests__/__snapshots__/script_transformer.test.js.snap b/packages/jest-transform/src/__tests__/__snapshots__/script_transformer.test.js.snap
index fe9bb5ceb3ec..b8d83f14fc5f 100644
--- a/packages/jest-transform/src/__tests__/__snapshots__/script_transformer.test.js.snap
+++ b/packages/jest-transform/src/__tests__/__snapshots__/script_transformer.test.js.snap
@@ -8,7 +8,12 @@ Object {
     "cache": true,
     "cacheDirectory": "/cache/",
     "clearMocks": false,
+    "collectCoverageFrom": Array [],
+    "collectCoverageOnlyFrom": null,
     "coveragePathIgnorePatterns": Array [],
+    "coverageThreshold": Object {
+      "global": Object {},
+    },
     "cwd": "/test_root_dir/",
     "detectLeaks": false,
     "detectOpenHandles": false,
@@ -228,7 +233,7 @@ exports[`ScriptTransformer uses multiple preprocessors 1`] = `
 const TRANSFORMED = {
   filename: '/fruits/banana.js',
   script: 'module.exports = "banana";',
-  config: '{"automock":false,"browser":false,"cache":true,"cacheDirectory":"/cache/","clearMocks":false,"coveragePathIgnorePatterns":[],"cwd":"/test_root_dir/","detectLeaks":false,"detectOpenHandles":false,"errorOnDeprecated":false,"extraGlobals":[],"filter":null,"forceCoverageMatch":[],"globalSetup":null,"globalTeardown":null,"globals":{},"haste":{"providesModuleNodeModules":[]},"moduleDirectories":[],"moduleFileExtensions":["js"],"moduleLoader":"/test_module_loader_path","moduleNameMapper":[],"modulePathIgnorePatterns":[],"modulePaths":[],"name":"test","prettierPath":"prettier","resetMocks":false,"resetModules":false,"resolver":null,"restoreMocks":false,"rootDir":"/","roots":[],"runner":"jest-runner","setupFiles":[],"setupFilesAfterEnv":[],"skipFilter":false,"skipNodeResolution":false,"snapshotResolver":null,"snapshotSerializers":[],"testEnvironment":"node","testEnvironmentOptions":{},"testLocationInResults":false,"testMatch":[],"testPathIgnorePatterns":[],"testRegex":["\\\\.test\\\\.js$"],"testRunner":"jest-jasmine2","testURL":"http://localhost","timers":"real","transform":[["^.+\\\\.js$","test_preprocessor"],["^.+\\\\.css$","css-preprocessor"]],"transformIgnorePatterns":["/node_modules/"],"unmockedModulePathPatterns":null,"watchPathIgnorePatterns":[]}',
+  config: '{"automock":false,"browser":false,"cache":true,"cacheDirectory":"/cache/","clearMocks":false,"collectCoverageFrom":[],"collectCoverageOnlyFrom":null,"coveragePathIgnorePatterns":[],"coverageThreshold":{"global":{}},"cwd":"/test_root_dir/","detectLeaks":false,"detectOpenHandles":false,"errorOnDeprecated":false,"extraGlobals":[],"filter":null,"forceCoverageMatch":[],"globalSetup":null,"globalTeardown":null,"globals":{},"haste":{"providesModuleNodeModules":[]},"moduleDirectories":[],"moduleFileExtensions":["js"],"moduleLoader":"/test_module_loader_path","moduleNameMapper":[],"modulePathIgnorePatterns":[],"modulePaths":[],"name":"test","prettierPath":"prettier","resetMocks":false,"resetModules":false,"resolver":null,"restoreMocks":false,"rootDir":"/","roots":[],"runner":"jest-runner","setupFiles":[],"setupFilesAfterEnv":[],"skipFilter":false,"skipNodeResolution":false,"snapshotResolver":null,"snapshotSerializers":[],"testEnvironment":"node","testEnvironmentOptions":{},"testLocationInResults":false,"testMatch":[],"testPathIgnorePatterns":[],"testRegex":["\\\\.test\\\\.js$"],"testRunner":"jest-jasmine2","testURL":"http://localhost","timers":"real","transform":[["^.+\\\\.js$","test_preprocessor"],["^.+\\\\.css$","css-preprocessor"]],"transformIgnorePatterns":["/node_modules/"],"unmockedModulePathPatterns":null,"watchPathIgnorePatterns":[]}',
 };
 `;
 
@@ -245,7 +250,7 @@ exports[`ScriptTransformer uses the supplied preprocessor 1`] = `
 const TRANSFORMED = {
   filename: '/fruits/banana.js',
   script: 'module.exports = "banana";',
-  config: '{"automock":false,"browser":false,"cache":true,"cacheDirectory":"/cache/","clearMocks":false,"coveragePathIgnorePatterns":[],"cwd":"/test_root_dir/","detectLeaks":false,"detectOpenHandles":false,"errorOnDeprecated":false,"extraGlobals":[],"filter":null,"forceCoverageMatch":[],"globalSetup":null,"globalTeardown":null,"globals":{},"haste":{"providesModuleNodeModules":[]},"moduleDirectories":[],"moduleFileExtensions":["js"],"moduleLoader":"/test_module_loader_path","moduleNameMapper":[],"modulePathIgnorePatterns":[],"modulePaths":[],"name":"test","prettierPath":"prettier","resetMocks":false,"resetModules":false,"resolver":null,"restoreMocks":false,"rootDir":"/","roots":[],"runner":"jest-runner","setupFiles":[],"setupFilesAfterEnv":[],"skipFilter":false,"skipNodeResolution":false,"snapshotResolver":null,"snapshotSerializers":[],"testEnvironment":"node","testEnvironmentOptions":{},"testLocationInResults":false,"testMatch":[],"testPathIgnorePatterns":[],"testRegex":["\\\\.test\\\\.js$"],"testRunner":"jest-jasmine2","testURL":"http://localhost","timers":"real","transform":[["^.+\\\\.js$","test_preprocessor"]],"transformIgnorePatterns":["/node_modules/"],"unmockedModulePathPatterns":null,"watchPathIgnorePatterns":[]}',
+  config: '{"automock":false,"browser":false,"cache":true,"cacheDirectory":"/cache/","clearMocks":false,"collectCoverageFrom":[],"collectCoverageOnlyFrom":null,"coveragePathIgnorePatterns":[],"coverageThreshold":{"global":{}},"cwd":"/test_root_dir/","detectLeaks":false,"detectOpenHandles":false,"errorOnDeprecated":false,"extraGlobals":[],"filter":null,"forceCoverageMatch":[],"globalSetup":null,"globalTeardown":null,"globals":{},"haste":{"providesModuleNodeModules":[]},"moduleDirectories":[],"moduleFileExtensions":["js"],"moduleLoader":"/test_module_loader_path","moduleNameMapper":[],"modulePathIgnorePatterns":[],"modulePaths":[],"name":"test","prettierPath":"prettier","resetMocks":false,"resetModules":false,"resolver":null,"restoreMocks":false,"rootDir":"/","roots":[],"runner":"jest-runner","setupFiles":[],"setupFilesAfterEnv":[],"skipFilter":false,"skipNodeResolution":false,"snapshotResolver":null,"snapshotSerializers":[],"testEnvironment":"node","testEnvironmentOptions":{},"testLocationInResults":false,"testMatch":[],"testPathIgnorePatterns":[],"testRegex":["\\\\.test\\\\.js$"],"testRunner":"jest-jasmine2","testURL":"http://localhost","timers":"real","transform":[["^.+\\\\.js$","test_preprocessor"]],"transformIgnorePatterns":["/node_modules/"],"unmockedModulePathPatterns":null,"watchPathIgnorePatterns":[]}',
 };
 `;
 
diff --git a/packages/jest-transform/src/__tests__/should_instrument.test.ts b/packages/jest-transform/src/__tests__/should_instrument.test.ts
index 1e1702d746f0..4e048f58e193 100644
--- a/packages/jest-transform/src/__tests__/should_instrument.test.ts
+++ b/packages/jest-transform/src/__tests__/should_instrument.test.ts
@@ -80,20 +80,22 @@ describe('shouldInstrument', () => {
     it('should return true when file is in collectCoverageOnlyFrom when provided', () => {
       testShouldInstrument(
         'collect/only/from/here.js',
+        {},
         {
+          ...defaultConfig,
           collectCoverageOnlyFrom: {'collect/only/from/here.js': true},
         },
-        defaultConfig,
       );
     });
 
     it('should return true when filename matches collectCoverageFrom', () => {
       testShouldInstrument(
         'do/collect/coverage.js',
+        {},
         {
+          ...defaultConfig,
           collectCoverageFrom: ['!**/dont/**/*.js', '**/do/**/*.js'],
         },
-        defaultConfig,
       );
     });
 
@@ -170,20 +172,22 @@ describe('shouldInstrument', () => {
     it('when file is not in collectCoverageOnlyFrom when provided', () => {
       testShouldInstrument(
         'source_file.js',
+        {},
         {
+          ...defaultConfig,
           collectCoverageOnlyFrom: {'collect/only/from/here.js': true},
         },
-        defaultConfig,
       );
     });
 
     it('when filename does not match collectCoverageFrom', () => {
       testShouldInstrument(
         'dont/collect/coverage.js',
+        {},
         {
+          ...defaultConfig,
           collectCoverageFrom: ['!**/dont/**/*.js', '**/do/**/*.js'],
         },
-        defaultConfig,
       );
     });
 
diff --git a/packages/jest-transform/src/shouldInstrument.ts b/packages/jest-transform/src/shouldInstrument.ts
index e9d75afdbc63..c2cf84facee4 100644
--- a/packages/jest-transform/src/shouldInstrument.ts
+++ b/packages/jest-transform/src/shouldInstrument.ts
@@ -49,19 +49,19 @@ export default function shouldInstrument(
   if (
     // This configuration field contains an object in the form of:
     // {'path/to/file.js': true}
-    options.collectCoverageOnlyFrom &&
-    !options.collectCoverageOnlyFrom[filename]
+    config.collectCoverageOnlyFrom &&
+    !config.collectCoverageOnlyFrom[filename]
   ) {
     return false;
   }
 
   if (
     // still cover if `only` is specified
-    !options.collectCoverageOnlyFrom &&
-    options.collectCoverageFrom.length &&
+    !config.collectCoverageOnlyFrom &&
+    config.collectCoverageFrom.length &&
     micromatch(
       [replacePathSepForGlob(path.relative(config.rootDir, filename))],
-      options.collectCoverageFrom,
+      config.collectCoverageFrom,
     ).length === 0
   ) {
     return false;
diff --git a/packages/jest-transform/src/types.ts b/packages/jest-transform/src/types.ts
index cfdfb97d4747..b093c879a4be 100644
--- a/packages/jest-transform/src/types.ts
+++ b/packages/jest-transform/src/types.ts
@@ -10,10 +10,7 @@ import type {Config} from '@jest/types';
 
 export type ShouldInstrumentOptions = Pick<
   Config.GlobalConfig,
-  | 'collectCoverage'
-  | 'collectCoverageFrom'
-  | 'collectCoverageOnlyFrom'
-  | 'coverageProvider'
+  'collectCoverage' | 'coverageProvider'
 > & {
   changedFiles?: Set<Config.Path>;
 };
diff --git a/packages/jest-types/src/Config.ts b/packages/jest-types/src/Config.ts
index 7169f8e13f18..77bfeece9cf0 100644
--- a/packages/jest-types/src/Config.ts
+++ b/packages/jest-types/src/Config.ts
@@ -226,7 +226,7 @@ export type CoverageThresholdValue = {
   statements?: number;
 };
 
-type CoverageThreshold = {
+export type CoverageThreshold = {
   [path: string]: CoverageThresholdValue;
   global: CoverageThresholdValue;
 };
@@ -236,15 +236,10 @@ export type GlobalConfig = {
   changedSince?: string;
   changedFilesWithAncestor: boolean;
   collectCoverage: boolean;
-  collectCoverageFrom: Array<Glob>;
-  collectCoverageOnlyFrom?: {
-    [key: string]: boolean;
-  };
   coverageDirectory: string;
   coveragePathIgnorePatterns?: Array<string>;
   coverageProvider: CoverageProvider;
   coverageReporters: Array<keyof ReportOptions | [keyof ReportOptions, any]>;
-  coverageThreshold?: CoverageThreshold;
   detectLeaks: boolean;
   detectOpenHandles: boolean;
   enabledTestsMap?: {
@@ -305,7 +300,12 @@ export type ProjectConfig = {
   cache: boolean;
   cacheDirectory: Path;
   clearMocks: boolean;
+  collectCoverageFrom: Array<Glob>;
+  collectCoverageOnlyFrom?: {
+    [key: string]: boolean;
+  };
   coveragePathIgnorePatterns: Array<string>;
+  coverageThreshold?: CoverageThreshold;
   cwd: Path;
   dependencyExtractor?: string;
   detectLeaks: boolean;
diff --git a/packages/jest-watcher/src/types.ts b/packages/jest-watcher/src/types.ts
index 4890c56b8f6e..7a31362c623b 100644
--- a/packages/jest-watcher/src/types.ts
+++ b/packages/jest-watcher/src/types.ts
@@ -50,8 +50,6 @@ export type AllowedConfigOptions = Partial<
     | 'bail'
     | 'changedSince'
     | 'collectCoverage'
-    | 'collectCoverageFrom'
-    | 'collectCoverageOnlyFrom'
     | 'coverageDirectory'
     | 'coverageReporters'
     | 'notify'