diff --git a/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts b/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts
index 89ecc0fc788d9..06fad1035d94e 100644
--- a/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts
+++ b/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts
@@ -58,6 +58,14 @@ describe('syncGenerator()', () => {
     });
   }
 
+  function addProjectWithImplicitDependencies(
+    name: string,
+    implicitDependencies: string[]
+  ) {
+    addProject(name);
+    projectGraph.nodes[name].data.implicitDependencies = implicitDependencies;
+  }
+
   beforeEach(async () => {
     tree = createTreeWithEmptyWorkspace();
     projectGraph = {
@@ -634,6 +642,23 @@ describe('syncGenerator()', () => {
       `);
     });
 
+    it('should not add a reference if dependent project is an implicit dependency', async () => {
+      addProject('implicit-dep');
+      addProjectWithImplicitDependencies('foo', ['implicit-dep']);
+
+      await syncGenerator(tree);
+
+      expect(tree.read('packages/foo/tsconfig.json').toString('utf-8'))
+        .toMatchInlineSnapshot(`
+        "{
+          "compilerOptions": {
+            "composite": true
+          }
+        }
+        "
+      `);
+    });
+
     describe('without custom sync generator options', () => {
       it.each`
         runtimeTsConfigFileName
diff --git a/packages/js/src/generators/typescript-sync/typescript-sync.ts b/packages/js/src/generators/typescript-sync/typescript-sync.ts
index e6825d8197c5f..751751ae63a1d 100644
--- a/packages/js/src/generators/typescript-sync/typescript-sync.ts
+++ b/packages/js/src/generators/typescript-sync/typescript-sync.ts
@@ -477,8 +477,8 @@ function collectProjectDependencies(
 
   for (const dep of projectGraph.dependencies[projectName]) {
     const targetProjectNode = projectGraph.nodes[dep.target];
-    if (!targetProjectNode) {
-      // It's an npm dependency
+    if (!targetProjectNode || dep.type === 'implicit') {
+      // It's an npm or an implicit dependency
       continue;
     }
 
diff --git a/packages/js/src/utils/typescript/ts-solution-setup.ts b/packages/js/src/utils/typescript/ts-solution-setup.ts
index 16df0733eb9cd..830e688b4ace5 100644
--- a/packages/js/src/utils/typescript/ts-solution-setup.ts
+++ b/packages/js/src/utils/typescript/ts-solution-setup.ts
@@ -183,17 +183,6 @@ export function updateTsconfigFiles(
     });
   }
 
-  if (tree.exists(tsconfigE2E)) {
-    // tsconfig.json for e2e projects need to have references array
-    updateJson(tree, tsconfigE2E, (json) => {
-      json.references ??= [];
-      const projectPath = relative(e2eRoot, projectRoot);
-      if (!json.references.some((x) => x.path === projectPath))
-        json.references.push({ path: projectPath });
-      return json;
-    });
-  }
-
   if (tree.exists('tsconfig.json')) {
     updateJson(tree, 'tsconfig.json', (json) => {
       const projectPath = './' + projectRoot;
diff --git a/packages/next/src/generators/application/application.spec.ts b/packages/next/src/generators/application/application.spec.ts
index b3bdb5a6bbd5e..2ea0cbbdcde39 100644
--- a/packages/next/src/generators/application/application.spec.ts
+++ b/packages/next/src/generators/application/application.spec.ts
@@ -1038,11 +1038,6 @@ describe('app (legacy)', () => {
             "**/*.cy.jsx",
             "**/*.d.ts",
           ],
-          "references": [
-            {
-              "path": "../myapp",
-            },
-          ],
         }
       `);
     });
diff --git a/packages/nuxt/src/generators/application/application.spec.ts b/packages/nuxt/src/generators/application/application.spec.ts
index a95f33cd0a323..aece521c022c9 100644
--- a/packages/nuxt/src/generators/application/application.spec.ts
+++ b/packages/nuxt/src/generators/application/application.spec.ts
@@ -362,11 +362,6 @@ describe('app', () => {
             "src/**/*.test.js",
             "src/**/*.d.ts",
           ],
-          "references": [
-            {
-              "path": "../myapp",
-            },
-          ],
         }
       `);
     });
diff --git a/packages/react/src/generators/application/application.spec.ts b/packages/react/src/generators/application/application.spec.ts
index 946dde33821c7..040cea110cb16 100644
--- a/packages/react/src/generators/application/application.spec.ts
+++ b/packages/react/src/generators/application/application.spec.ts
@@ -1447,11 +1447,6 @@ describe('app', () => {
             "src/**/*.test.js",
             "src/**/*.d.ts",
           ],
-          "references": [
-            {
-              "path": "../myapp",
-            },
-          ],
         }
       `);
     });
diff --git a/packages/remix/src/generators/application/application.impl.spec.ts b/packages/remix/src/generators/application/application.impl.spec.ts
index 60319d57a2975..4d3ca33870dc0 100644
--- a/packages/remix/src/generators/application/application.impl.spec.ts
+++ b/packages/remix/src/generators/application/application.impl.spec.ts
@@ -522,11 +522,6 @@ describe('Remix Application', () => {
             "src/**/*.test.js",
             "src/**/*.d.ts",
           ],
-          "references": [
-            {
-              "path": "../myapp",
-            },
-          ],
         }
       `);
     });