diff --git a/packages/nx/src/generators/utils/project-configuration.spec.ts b/packages/nx/src/generators/utils/project-configuration.spec.ts
index c96e4daaf0fa6..bec512e7ba3c4 100644
--- a/packages/nx/src/generators/utils/project-configuration.spec.ts
+++ b/packages/nx/src/generators/utils/project-configuration.spec.ts
@@ -329,5 +329,46 @@ describe('project configuration', () => {
       `);
       expect(tree.exists('proj/project.json')).toBeFalsy();
     });
+
+    it('should avoid writing empty nx property', () => {
+      writeJson(tree, 'proj/package.json', {
+        name: 'proj',
+      });
+
+      updateProjectConfiguration(tree, 'proj', {
+        root: 'proj',
+      });
+
+      const updatedProj = readProjectConfiguration(tree, 'proj');
+      expect(updatedProj).toEqual({
+        name: 'proj',
+        root: 'proj',
+      });
+
+      expect(tree.read('proj/package.json', 'utf-8')).toMatchInlineSnapshot(`
+        "{
+          "name": "proj"
+        }
+        "
+      `);
+      expect(tree.exists('proj/project.json')).toBeFalsy();
+
+      // Adding tags will add nx property
+      updateProjectConfiguration(tree, 'proj', {
+        root: 'proj',
+        tags: ['test'],
+      });
+      expect(tree.read('proj/package.json', 'utf-8')).toMatchInlineSnapshot(`
+        "{
+          "name": "proj",
+          "nx": {
+            "tags": [
+              "test"
+            ]
+          }
+        }
+        "
+      `);
+    });
   });
 });
diff --git a/packages/nx/src/generators/utils/project-configuration.ts b/packages/nx/src/generators/utils/project-configuration.ts
index 5011db23a4b46..0eec94fa4515d 100644
--- a/packages/nx/src/generators/utils/project-configuration.ts
+++ b/packages/nx/src/generators/utils/project-configuration.ts
@@ -130,10 +130,19 @@ function updateProjectConfigurationInPackageJson(
   packageJson.nx = {
     ...packageJson.nx,
     ...projectConfiguration,
-    root: undefined,
   };
 
-  writeJson(tree, packageJsonFile, packageJson);
+  // We don't want to ever this since it is inferred
+  delete packageJson.nx.root;
+
+  // Only set `nx` property in `package.json` if it is a root project (necessary to mark it as Nx project),
+  // or if there are properties to be set. If it is empty, then avoid it so we don't add unnecessary boilerplate.
+  if (
+    projectConfiguration.root === '.' ||
+    Object.keys(packageJson.nx).length > 0
+  ) {
+    writeJson(tree, packageJsonFile, packageJson);
+  }
 }
 
 function updateProjectConfigurationInProjectJson(
@@ -245,8 +254,15 @@ function readAndCombineAllProjectConfigurations(tree: Tree): {
   const patterns = [
     '**/project.json',
     'project.json',
-    ...getGlobPatternsFromPackageManagerWorkspaces(tree.root, (p) =>
-      readJson(tree, p, { expectComments: true })
+    ...getGlobPatternsFromPackageManagerWorkspaces(
+      tree.root,
+      (p) => readJson(tree, p, { expectComments: true }),
+      <T extends Object>(p) => {
+        const content = tree.read(p, 'utf-8');
+        const { load } = require('@zkochan/js-yaml');
+        return load(content, { filename: p }) as T;
+      },
+      (p) => tree.exists(p)
     ),
   ];
   const globbedFiles = globWithWorkspaceContextSync(tree.root, patterns);
diff --git a/packages/nx/src/plugins/package-json/create-nodes.ts b/packages/nx/src/plugins/package-json/create-nodes.ts
index e30202d053def..66c9128026013 100644
--- a/packages/nx/src/plugins/package-json/create-nodes.ts
+++ b/packages/nx/src/plugins/package-json/create-nodes.ts
@@ -237,8 +237,14 @@ export function buildProjectConfigurationFromPackageJson(
  */
 export function getGlobPatternsFromPackageManagerWorkspaces(
   root: string,
-  readJson: <T extends Object>(path: string) => T = <T extends Object>(path) =>
-    readJsonFile<T>(join(root, path)) // making this an arg allows us to reuse in devkit
+  // allow overwriting these args so we can use them in devkit
+  readJson: <T extends Object>(path: string) => T = <T extends Object>(
+    path: string
+  ) => readJsonFile<T>(join(root, path)),
+  readYaml: <T extends Object>(path: string) => T = <T extends Object>(
+    path: string
+  ) => readYamlFile<T>(join(root, path)),
+  exists: (path: string) => boolean = (p) => existsSync(join(root, p))
 ): string[] {
   try {
     const patterns: string[] = [];
@@ -252,12 +258,10 @@ export function getGlobPatternsFromPackageManagerWorkspaces(
       )
     );
 
-    if (existsSync(join(root, 'pnpm-workspace.yaml'))) {
+    if (exists('pnpm-workspace.yaml')) {
       try {
         const { packages } =
-          readYamlFile<{ packages: string[] }>(
-            join(root, 'pnpm-workspace.yaml')
-          ) ?? {};
+          readYaml<{ packages: string[] }>('pnpm-workspace.yaml') ?? {};
         patterns.push(...normalizePatterns(packages || []));
       } catch (e: unknown) {
         output.warn({