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 a3e07268cd..a01f3ca306 100644
--- a/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts
+++ b/packages/js/src/generators/typescript-sync/typescript-sync.spec.ts
@@ -371,12 +371,19 @@ describe('syncGenerator()', () => {
           { path: '../c' }, // this is not a dependency, should be pruned
         ],
       });
+      // add a project with no dependencies
+      addProject('c');
+      updateJson(tree, 'packages/c/tsconfig.json', (json) => {
+        // this is not a dependency, should be pruned
+        json.references = [{ path: '../d' }];
+        return json;
+      });
 
       await syncGenerator(tree);
 
-      const rootTsconfig = readJson(tree, 'packages/b/tsconfig.json');
+      const bTsconfigJson = readJson(tree, 'packages/b/tsconfig.json');
       // The dependency reference on "a" is added to the start of the array
-      expect(rootTsconfig.references).toMatchInlineSnapshot(`
+      expect(bTsconfigJson.references).toMatchInlineSnapshot(`
         [
           {
             "path": "../a",
@@ -389,6 +396,8 @@ describe('syncGenerator()', () => {
           },
         ]
       `);
+      const cTsconfigJson = readJson(tree, 'packages/c/tsconfig.json');
+      expect(cTsconfigJson.references).toStrictEqual([]);
     });
 
     it('should not prune existing external project references that are not dependencies but are git ignored', async () => {
diff --git a/packages/js/src/generators/typescript-sync/typescript-sync.ts b/packages/js/src/generators/typescript-sync/typescript-sync.ts
index 2c54033d5a..75469689a4 100644
--- a/packages/js/src/generators/typescript-sync/typescript-sync.ts
+++ b/packages/js/src/generators/typescript-sync/typescript-sync.ts
@@ -176,8 +176,7 @@ export async function syncGenerator(tree: Tree): Promise<SyncGeneratorResult> {
   for (const [projectName, data] of Object.entries(projectGraph.dependencies)) {
     if (
       !projectGraph.nodes[projectName] ||
-      projectGraph.nodes[projectName].data.root === '.' ||
-      !data.length
+      projectGraph.nodes[projectName].data.root === '.'
     ) {
       continue;
     }
@@ -208,9 +207,6 @@ export async function syncGenerator(tree: Tree): Promise<SyncGeneratorResult> {
       projectGraph,
       collectedDependencies
     );
-    if (!dependencies.length) {
-      continue;
-    }
 
     for (const runtimeTsConfigFileName of runtimeTsConfigFileNames) {
       const runtimeTsConfigPath = joinPathFragments(
diff --git a/packages/js/src/plugins/typescript/plugin.spec.ts b/packages/js/src/plugins/typescript/plugin.spec.ts
index afe458817b..0e97fb30d8 100644
--- a/packages/js/src/plugins/typescript/plugin.spec.ts
+++ b/packages/js/src/plugins/typescript/plugin.spec.ts
@@ -443,6 +443,19 @@ describe(`Plugin: ${PLUGIN_NAME}`, () => {
       `);
     });
 
+    it('should handle ts project references pointing to non-existing files and not throw', async () => {
+      await applyFilesToTempFsAndContext(tempFs, context, {
+        'libs/my-lib/tsconfig.json': JSON.stringify({
+          references: [{ path: '../my-lib-2' }],
+        }),
+        'libs/my-lib/package.json': `{}`,
+      });
+
+      await expect(
+        invokeCreateNodesOnMatchingFiles(context, {})
+      ).resolves.not.toThrow();
+    });
+
     describe('inputs', () => {
       it('should add the config file and the `include` and `exclude` patterns', async () => {
         await applyFilesToTempFsAndContext(tempFs, context, {
@@ -1821,6 +1834,23 @@ describe(`Plugin: ${PLUGIN_NAME}`, () => {
       `);
     });
 
+    it('should handle ts project references pointing to non-existing files and not throw', async () => {
+      await applyFilesToTempFsAndContext(tempFs, context, {
+        'libs/my-lib/tsconfig.json': JSON.stringify({
+          references: [{ path: '../my-lib-2' }],
+        }),
+        'libs/my-lib/tsconfig.lib.json': `{}`,
+        'libs/my-lib/package.json': `{}`,
+      });
+
+      await expect(
+        invokeCreateNodesOnMatchingFiles(context, {
+          typecheck: false,
+          build: true,
+        })
+      ).resolves.not.toThrow();
+    });
+
     describe('inputs', () => {
       it('should add the config file and the `include` and `exclude` patterns', async () => {
         await applyFilesToTempFsAndContext(tempFs, context, {
diff --git a/packages/js/src/plugins/typescript/plugin.ts b/packages/js/src/plugins/typescript/plugin.ts
index 09bbe98822..2ec1ba459e 100644
--- a/packages/js/src/plugins/typescript/plugin.ts
+++ b/packages/js/src/plugins/typescript/plugin.ts
@@ -545,6 +545,11 @@ function resolveInternalProjectReferences(
       continue;
     }
 
+    if (!existsSync(refConfigPath)) {
+      // the referenced tsconfig doesn't exist, ignore it
+      continue;
+    }
+
     if (isExternalProjectReference(refConfigPath, workspaceRoot, projectRoot)) {
       continue;
     }
@@ -585,6 +590,11 @@ function hasExternalProjectReferences(
       continue;
     }
 
+    if (!existsSync(refConfigPath)) {
+      // the referenced tsconfig doesn't exist, ignore it
+      continue;
+    }
+
     if (isExternalProjectReference(refConfigPath, workspaceRoot, projectRoot)) {
       return true;
     }