diff --git a/docs/guide/workspace.md b/docs/guide/workspace.md
index 69e80b79d0fa..8f55882b2c64 100644
--- a/docs/guide/workspace.md
+++ b/docs/guide/workspace.md
@@ -231,6 +231,4 @@ All configuration options that are not supported inside a project config have <N
 
 ## Coverage
 
-Coverage for workspace projects works out of the box. But if you have [`all`](/config/#coverage-all) option enabled and use non-conventional extensions in some of your projects, you will need to have a plugin that handles this extension in your root configuration file.
-
-For example, if you have a package that uses Vue files and it has its own config file, but some of the files are not imported in your tests, coverage will fail trying to analyze the usage of unused files, because it relies on the root configuration rather than project configuration.
+Coverage for workspace projects works out of the box.
diff --git a/packages/coverage-istanbul/src/provider.ts b/packages/coverage-istanbul/src/provider.ts
index 0dd865631633..d3a8bd207727 100644
--- a/packages/coverage-istanbul/src/provider.ts
+++ b/packages/coverage-istanbul/src/provider.ts
@@ -414,13 +414,15 @@ export class IstanbulCoverageProvider extends BaseCoverageProvider implements Co
     const cacheKey = new Date().getTime()
     const coverageMap = libCoverage.createCoverageMap({})
 
+    const transform = this.createUncoveredFileTransformer(this.ctx)
+
     // Note that these cannot be run parallel as synchronous instrumenter.lastFileCoverage
     // returns the coverage of the last transformed file
     for (const [index, filename] of uncoveredFiles.entries()) {
       debug('Uncovered file %s %d/%d', filename, index, uncoveredFiles.length)
 
       // Make sure file is not served from cache so that instrumenter loads up requested file coverage
-      await this.ctx.vitenode.transformRequest(`${filename}?v=${cacheKey}`)
+      await transform(`${filename}?v=${cacheKey}`)
       const lastCoverage = this.instrumenter.lastFileCoverage()
       coverageMap.addFileCoverage(lastCoverage)
     }
diff --git a/packages/coverage-v8/src/provider.ts b/packages/coverage-v8/src/provider.ts
index b6b0f8708b73..92de2b7f7779 100644
--- a/packages/coverage-v8/src/provider.ts
+++ b/packages/coverage-v8/src/provider.ts
@@ -368,6 +368,7 @@ export class V8CoverageProvider extends BaseCoverageProvider implements Coverage
     const transformResults = normalizeTransformResults(
       this.ctx.vitenode.fetchCache,
     )
+    const transform = this.createUncoveredFileTransformer(this.ctx)
 
     const allFiles = await this.testExclude.glob(this.ctx.config.root)
     let includedFiles = allFiles.map(file =>
@@ -401,7 +402,7 @@ export class V8CoverageProvider extends BaseCoverageProvider implements Coverage
           const { originalSource } = await this.getSources(
             filename.href,
             transformResults,
-            file => this.ctx.vitenode.transformRequest(file),
+            transform,
           )
 
           const coverage = {
diff --git a/packages/vitest/src/utils/coverage.ts b/packages/vitest/src/utils/coverage.ts
index 4d40855fdd6e..285a2ba59299 100644
--- a/packages/vitest/src/utils/coverage.ts
+++ b/packages/vitest/src/utils/coverage.ts
@@ -1,6 +1,7 @@
 import { relative } from 'pathe'
 import mm from 'micromatch'
 import type { CoverageMap } from 'istanbul-lib-coverage'
+import type { Vitest } from '../node/core'
 import type { BaseCoverageOptions, ResolvedCoverageOptions } from '../node/types/coverage'
 import { resolveCoverageReporters } from '../node/config/resolveConfig'
 
@@ -272,6 +273,37 @@ export class BaseCoverageProvider {
       return chunks
     }, [])
   }
+
+  createUncoveredFileTransformer(ctx: Vitest) {
+    const servers = [
+      ...ctx.projects.map(project => ({
+        root: project.config.root,
+        vitenode: project.vitenode,
+      })),
+      // Check core last as it will match all files anyway
+      { root: ctx.config.root, vitenode: ctx.vitenode },
+    ]
+
+    return async function transformFile(filename: string) {
+      let lastError
+
+      for (const { root, vitenode } of servers) {
+        if (!filename.startsWith(root)) {
+          continue
+        }
+
+        try {
+          return await vitenode.transformRequest(filename)
+        }
+        catch (error) {
+          lastError = error
+        }
+      }
+
+      // All vite-node servers failed to transform the file
+      throw lastError
+    }
+  }
 }
 
 /**
diff --git a/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts b/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts
new file mode 100644
index 000000000000..507ede9cf27c
--- /dev/null
+++ b/test/coverage-test/fixtures/configs/vitest.workspace.multi-transforms.ts
@@ -0,0 +1,78 @@
+import { readFileSync } from "node:fs";
+import { Plugin, defineWorkspace } from "vitest/config";
+import MagicString from "magic-string";
+
+export default defineWorkspace([
+  // Project that uses its own "root" and custom transform plugin
+  {
+    test: {
+      name: "custom-with-root",
+      root: "fixtures/workspaces/custom-2",
+    },
+    plugins: [customFilePlugin("2")],
+  },
+
+  // Project that cannot transform "*.custom-x" files
+  {
+    test: {
+      name: "normal",
+      include: ["fixtures/test/math.test.ts"],
+    },
+  },
+
+  // Project that uses default "root" and has custom transform plugin
+  {
+    test: {
+      name: "custom",
+      include: ["fixtures/test/custom-1-syntax.test.ts"],
+    },
+    plugins: [customFilePlugin("1")],
+  },
+]);
+
+/**
+ * Plugin for transforming `.custom-1` and/or `.custom-2` files to Javascript
+ */
+function customFilePlugin(postfix: "1" | "2"): Plugin {
+  function transform(code: MagicString) {
+    code.replaceAll(
+      "<function covered>",
+      `
+function covered() {
+  return "Custom-${postfix} file loaded!"
+}
+  `.trim()
+    );
+
+    code.replaceAll(
+      "<function uncovered>",
+      `
+function uncovered() {
+  return "This should be uncovered!"
+}
+    `.trim()
+    );
+
+    code.replaceAll("<default export covered>", "export default covered()");
+    code.replaceAll("<default export uncovered>", "export default uncovered()");
+  }
+
+  return {
+    name: `custom-${postfix}-file-plugin`,
+    transform(_, id) {
+      const filename = id.split("?")[0];
+
+      if (filename.endsWith(`.custom-${postfix}`)) {
+        const content = readFileSync(filename, "utf8");
+
+        const s = new MagicString(content);
+        transform(s);
+
+        return {
+          code: s.toString(),
+          map: s.generateMap({ hires: "boundary" }),
+        };
+      }
+    },
+  };
+}
diff --git a/test/coverage-test/fixtures/src/covered.custom-1 b/test/coverage-test/fixtures/src/covered.custom-1
new file mode 100644
index 000000000000..095b52aa44c8
--- /dev/null
+++ b/test/coverage-test/fixtures/src/covered.custom-1
@@ -0,0 +1,5 @@
+<function covered>
+
+<function uncovered>
+
+<default export covered>
diff --git a/test/coverage-test/fixtures/src/uncovered.custom-1 b/test/coverage-test/fixtures/src/uncovered.custom-1
new file mode 100644
index 000000000000..f4e16be2968b
--- /dev/null
+++ b/test/coverage-test/fixtures/src/uncovered.custom-1
@@ -0,0 +1,3 @@
+<function uncovered>
+
+<default export uncovered>
diff --git a/test/coverage-test/fixtures/test/custom-1-syntax.test.ts b/test/coverage-test/fixtures/test/custom-1-syntax.test.ts
new file mode 100644
index 000000000000..6da0aea4b553
--- /dev/null
+++ b/test/coverage-test/fixtures/test/custom-1-syntax.test.ts
@@ -0,0 +1,8 @@
+import { expect, test } from 'vitest'
+
+// @ts-expect-error -- untyped
+import output from '../src/covered.custom-1'
+
+test('custom file loads fine', () => {
+  expect(output).toMatch('Custom-1 file loaded!')
+})
diff --git a/test/coverage-test/fixtures/workspaces/custom-2/src/covered.custom-2 b/test/coverage-test/fixtures/workspaces/custom-2/src/covered.custom-2
new file mode 100644
index 000000000000..095b52aa44c8
--- /dev/null
+++ b/test/coverage-test/fixtures/workspaces/custom-2/src/covered.custom-2
@@ -0,0 +1,5 @@
+<function covered>
+
+<function uncovered>
+
+<default export covered>
diff --git a/test/coverage-test/fixtures/workspaces/custom-2/src/uncovered.custom-2 b/test/coverage-test/fixtures/workspaces/custom-2/src/uncovered.custom-2
new file mode 100644
index 000000000000..f4e16be2968b
--- /dev/null
+++ b/test/coverage-test/fixtures/workspaces/custom-2/src/uncovered.custom-2
@@ -0,0 +1,3 @@
+<function uncovered>
+
+<default export uncovered>
diff --git a/test/coverage-test/fixtures/workspaces/custom-2/test/custom-2-syntax.test.ts b/test/coverage-test/fixtures/workspaces/custom-2/test/custom-2-syntax.test.ts
new file mode 100644
index 000000000000..ffc0d6c55b6e
--- /dev/null
+++ b/test/coverage-test/fixtures/workspaces/custom-2/test/custom-2-syntax.test.ts
@@ -0,0 +1,8 @@
+import { expect, test } from 'vitest'
+
+// @ts-expect-error -- untyped
+import output from '../src/covered.custom-2'
+
+test('custom-2 file loads fine', () => {
+  expect(output).toMatch('Custom-2 file loaded!')
+})
diff --git a/test/coverage-test/test/__snapshots__/custom-file-covered-1-istanbul.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-covered-1-istanbul.snapshot.json
new file mode 100644
index 000000000000..8ebdab27587b
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-covered-1-istanbul.snapshot.json
@@ -0,0 +1,83 @@
+{
+  "path": "<process-cwd>/fixtures/src/covered.custom-1",
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 18
+      }
+    },
+    "1": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 20
+      }
+    }
+  },
+  "fnMap": {
+    "0": {
+      "name": "covered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      }
+    },
+    "1": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      }
+    }
+  },
+  "branchMap": {},
+  "s": {
+    "0": 1,
+    "1": 0
+  },
+  "f": {
+    "0": 1,
+    "1": 0
+  },
+  "b": {}
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-covered-1-v8.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-covered-1-v8.snapshot.json
new file mode 100644
index 000000000000..35a17c7894b8
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-covered-1-v8.snapshot.json
@@ -0,0 +1,150 @@
+{
+  "path": "<process-cwd>/fixtures/src/covered.custom-1",
+  "all": false,
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 18
+      }
+    },
+    "1": {
+      "start": {
+        "line": 2,
+        "column": 0
+      },
+      "end": {
+        "line": 2,
+        "column": 0
+      }
+    },
+    "2": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 20
+      }
+    },
+    "3": {
+      "start": {
+        "line": 4,
+        "column": 0
+      },
+      "end": {
+        "line": 4,
+        "column": 0
+      }
+    },
+    "4": {
+      "start": {
+        "line": 5,
+        "column": 0
+      },
+      "end": {
+        "line": 5,
+        "column": 24
+      }
+    }
+  },
+  "s": {
+    "0": 1,
+    "1": 1,
+    "2": 0,
+    "3": 1,
+    "4": 1
+  },
+  "branchMap": {
+    "0": {
+      "type": "branch",
+      "line": 1,
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "locations": [
+        {
+          "start": {
+            "line": 1,
+            "column": 0
+          },
+          "end": {
+            "line": 1,
+            "column": 18
+          }
+        }
+      ]
+    }
+  },
+  "b": {
+    "0": [
+      1
+    ]
+  },
+  "fnMap": {
+    "0": {
+      "name": "covered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "line": 1
+    },
+    "1": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "line": 3
+    }
+  },
+  "f": {
+    "0": 1,
+    "1": 0
+  }
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-covered-2-istanbul.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-covered-2-istanbul.snapshot.json
new file mode 100644
index 000000000000..996a4a66c39e
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-covered-2-istanbul.snapshot.json
@@ -0,0 +1,83 @@
+{
+  "path": "<process-cwd>/fixtures/workspaces/custom-2/src/covered.custom-2",
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 18
+      }
+    },
+    "1": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 20
+      }
+    }
+  },
+  "fnMap": {
+    "0": {
+      "name": "covered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      }
+    },
+    "1": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      }
+    }
+  },
+  "branchMap": {},
+  "s": {
+    "0": 1,
+    "1": 0
+  },
+  "f": {
+    "0": 1,
+    "1": 0
+  },
+  "b": {}
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-covered-2-v8.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-covered-2-v8.snapshot.json
new file mode 100644
index 000000000000..e5380af0ec31
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-covered-2-v8.snapshot.json
@@ -0,0 +1,150 @@
+{
+  "path": "<process-cwd>/fixtures/workspaces/custom-2/src/covered.custom-2",
+  "all": false,
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 18
+      }
+    },
+    "1": {
+      "start": {
+        "line": 2,
+        "column": 0
+      },
+      "end": {
+        "line": 2,
+        "column": 0
+      }
+    },
+    "2": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 20
+      }
+    },
+    "3": {
+      "start": {
+        "line": 4,
+        "column": 0
+      },
+      "end": {
+        "line": 4,
+        "column": 0
+      }
+    },
+    "4": {
+      "start": {
+        "line": 5,
+        "column": 0
+      },
+      "end": {
+        "line": 5,
+        "column": 24
+      }
+    }
+  },
+  "s": {
+    "0": 1,
+    "1": 1,
+    "2": 0,
+    "3": 1,
+    "4": 1
+  },
+  "branchMap": {
+    "0": {
+      "type": "branch",
+      "line": 1,
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "locations": [
+        {
+          "start": {
+            "line": 1,
+            "column": 0
+          },
+          "end": {
+            "line": 1,
+            "column": 18
+          }
+        }
+      ]
+    }
+  },
+  "b": {
+    "0": [
+      1
+    ]
+  },
+  "fnMap": {
+    "0": {
+      "name": "covered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 18
+        }
+      },
+      "line": 1
+    },
+    "1": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 3,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 20
+        }
+      },
+      "line": 3
+    }
+  },
+  "f": {
+    "0": 1,
+    "1": 0
+  }
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-istanbul.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-istanbul.snapshot.json
new file mode 100644
index 000000000000..af9efc13611e
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-istanbul.snapshot.json
@@ -0,0 +1,48 @@
+{
+  "path": "<process-cwd>/fixtures/src/uncovered.custom-1",
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 20
+      }
+    }
+  },
+  "fnMap": {
+    "0": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 20
+        }
+      }
+    }
+  },
+  "branchMap": {},
+  "s": {
+    "0": 0
+  },
+  "f": {
+    "0": 0
+  },
+  "b": {}
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-v8.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-v8.snapshot.json
new file mode 100644
index 000000000000..1eed60fca928
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-uncovered-1-v8.snapshot.json
@@ -0,0 +1,103 @@
+{
+  "path": "<process-cwd>/fixtures/src/uncovered.custom-1",
+  "all": true,
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 20
+      }
+    },
+    "1": {
+      "start": {
+        "line": 2,
+        "column": 0
+      },
+      "end": {
+        "line": 2,
+        "column": 0
+      }
+    },
+    "2": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 26
+      }
+    }
+  },
+  "s": {
+    "0": 0,
+    "1": 0,
+    "2": 0
+  },
+  "branchMap": {
+    "0": {
+      "type": "branch",
+      "line": 1,
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "locations": [
+        {
+          "start": {
+            "line": 1,
+            "column": 0
+          },
+          "end": {
+            "line": 3,
+            "column": 26
+          }
+        }
+      ]
+    }
+  },
+  "b": {
+    "0": [
+      0
+    ]
+  },
+  "fnMap": {
+    "0": {
+      "name": "(empty-report)",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "line": 1
+    }
+  },
+  "f": {
+    "0": 0
+  }
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-istanbul.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-istanbul.snapshot.json
new file mode 100644
index 000000000000..eb4119bb3faa
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-istanbul.snapshot.json
@@ -0,0 +1,48 @@
+{
+  "path": "<process-cwd>/fixtures/workspaces/custom-2/src/uncovered.custom-2",
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 20
+      }
+    }
+  },
+  "fnMap": {
+    "0": {
+      "name": "uncovered",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 20
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 1,
+          "column": 20
+        }
+      }
+    }
+  },
+  "branchMap": {},
+  "s": {
+    "0": 0
+  },
+  "f": {
+    "0": 0
+  },
+  "b": {}
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-v8.snapshot.json b/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-v8.snapshot.json
new file mode 100644
index 000000000000..4d6d12368463
--- /dev/null
+++ b/test/coverage-test/test/__snapshots__/custom-file-uncovered-2-v8.snapshot.json
@@ -0,0 +1,103 @@
+{
+  "path": "<process-cwd>/fixtures/workspaces/custom-2/src/uncovered.custom-2",
+  "all": true,
+  "statementMap": {
+    "0": {
+      "start": {
+        "line": 1,
+        "column": 0
+      },
+      "end": {
+        "line": 1,
+        "column": 20
+      }
+    },
+    "1": {
+      "start": {
+        "line": 2,
+        "column": 0
+      },
+      "end": {
+        "line": 2,
+        "column": 0
+      }
+    },
+    "2": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 3,
+        "column": 26
+      }
+    }
+  },
+  "s": {
+    "0": 0,
+    "1": 0,
+    "2": 0
+  },
+  "branchMap": {
+    "0": {
+      "type": "branch",
+      "line": 1,
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "locations": [
+        {
+          "start": {
+            "line": 1,
+            "column": 0
+          },
+          "end": {
+            "line": 3,
+            "column": 26
+          }
+        }
+      ]
+    }
+  },
+  "b": {
+    "0": [
+      0
+    ]
+  },
+  "fnMap": {
+    "0": {
+      "name": "(empty-report)",
+      "decl": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "loc": {
+        "start": {
+          "line": 1,
+          "column": 0
+        },
+        "end": {
+          "line": 3,
+          "column": 26
+        }
+      },
+      "line": 1
+    }
+  },
+  "f": {
+    "0": 0
+  }
+}
\ No newline at end of file
diff --git a/test/coverage-test/test/all.test.ts b/test/coverage-test/test/all.test.ts
index 063072e1f3db..97e464ed80af 100644
--- a/test/coverage-test/test/all.test.ts
+++ b/test/coverage-test/test/all.test.ts
@@ -4,7 +4,7 @@ import { readCoverageMap, runVitest, test } from '../utils'
 test('{ all: true } includes uncovered files', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
-    exclude: ['**/virtual-files-**'],
+    exclude: ['**/virtual-files-**', '**/custom-1-syntax**'],
     coverage: {
       include: ['fixtures/src/**'],
       all: true,
@@ -25,7 +25,7 @@ test('{ all: true } includes uncovered files', async () => {
 test('{ all: false } excludes uncovered files', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
-    exclude: ['**/virtual-files-**'],
+    exclude: ['**/virtual-files-**', '**/custom-1-syntax**'],
     coverage: {
       include: ['fixtures/src/**'],
       all: false,
diff --git a/test/coverage-test/test/changed.test.ts b/test/coverage-test/test/changed.test.ts
index ada4a686306d..78083beec26c 100644
--- a/test/coverage-test/test/changed.test.ts
+++ b/test/coverage-test/test/changed.test.ts
@@ -33,6 +33,7 @@ afterAll(() => {
 test('{ changed: "HEAD" }', async () => {
   await runVitest({
     include: ['fixtures/test/**'],
+    exclude: ['**/custom-1-syntax**'],
     changed: 'HEAD',
     coverage: {
       include: ['fixtures/src/**'],
diff --git a/test/coverage-test/test/workspace.multi-transform.test.ts b/test/coverage-test/test/workspace.multi-transform.test.ts
new file mode 100644
index 000000000000..0eb2b63df398
--- /dev/null
+++ b/test/coverage-test/test/workspace.multi-transform.test.ts
@@ -0,0 +1,43 @@
+import { expect } from 'vitest'
+import { isV8Provider, readCoverageMap, runVitest, test } from '../utils'
+
+test('{ all: true } includes uncovered files that require custom transform', async () => {
+  await runVitest({
+    workspace: 'fixtures/configs/vitest.workspace.multi-transforms.ts',
+    coverage: {
+      all: true,
+      extension: ['.ts', '.custom-1', '.custom-2'],
+      reporter: ['json', 'html'],
+      include: ['**/*.custom-1', '**/*.custom-2', '**/math.ts'],
+    },
+  })
+
+  const coverageMap = await readCoverageMap()
+  const files = coverageMap.files()
+
+  // All files from workspace should be picked
+  expect(files).toMatchInlineSnapshot(`
+    [
+      "<process-cwd>/fixtures/src/covered.custom-1",
+      "<process-cwd>/fixtures/src/math.ts",
+      "<process-cwd>/fixtures/src/uncovered.custom-1",
+      "<process-cwd>/fixtures/workspaces/custom-2/src/covered.custom-2",
+      "<process-cwd>/fixtures/workspaces/custom-2/src/uncovered.custom-2",
+    ]
+  `)
+
+  const covered1 = coverageMap.fileCoverageFor('<process-cwd>/fixtures/src/covered.custom-1')
+  const uncovered1 = coverageMap.fileCoverageFor('<process-cwd>/fixtures/src/uncovered.custom-1')
+  const covered2 = coverageMap.fileCoverageFor('<process-cwd>/fixtures/workspaces/custom-2/src/covered.custom-2')
+  const uncovered2 = coverageMap.fileCoverageFor('<process-cwd>/fixtures/workspaces/custom-2/src/uncovered.custom-2')
+
+  // Coverage maps indicate whether source maps are correct. Check html-report if these change
+  expect(JSON.stringify(covered1, null, 2)).toMatchFileSnapshot(snapshotName('covered-1'))
+  expect(JSON.stringify(uncovered1, null, 2)).toMatchFileSnapshot(snapshotName('uncovered-1'))
+  expect(JSON.stringify(covered2, null, 2)).toMatchFileSnapshot(snapshotName('covered-2'))
+  expect(JSON.stringify(uncovered2, null, 2)).toMatchFileSnapshot(snapshotName('uncovered-2'))
+})
+
+function snapshotName(label: string) {
+  return `__snapshots__/custom-file-${label}-${isV8Provider() ? 'v8' : 'istanbul'}.snapshot.json`
+}