diff --git a/packages/nx/src/project-graph/utils/project-configuration-utils.spec.ts b/packages/nx/src/project-graph/utils/project-configuration-utils.spec.ts
index ba16b50b938aef..d3ca5ecabca8b1 100644
--- a/packages/nx/src/project-graph/utils/project-configuration-utils.spec.ts
+++ b/packages/nx/src/project-graph/utils/project-configuration-utils.spec.ts
@@ -965,6 +965,47 @@ describe('project-configuration-utils', () => {
           sourceMap['libs/lib-a']['metadata.targetGroups.group1.1']
         ).toEqual(['dummy', 'dummy.ts']);
       });
+
+      it('should not clobber targetGroups', () => {
+        const rootMap = new RootMapBuilder()
+          .addProject({
+            root: 'libs/lib-a',
+            name: 'lib-a',
+            metadata: {
+              targetGroups: {
+                group2: ['target3'],
+              },
+            },
+          })
+          .getRootMap();
+        const sourceMap: ConfigurationSourceMaps = {
+          'libs/lib-a': {},
+        };
+
+        mergeProjectConfigurationIntoRootMap(
+          rootMap,
+          {
+            root: 'libs/lib-a',
+            name: 'lib-a',
+            metadata: {
+              technologies: ['technology'],
+              targetGroups: {
+                group1: ['target1', 'target2'],
+              },
+            },
+          },
+          sourceMap,
+          ['dummy', 'dummy.ts']
+        );
+
+        expect(rootMap['libs/lib-a'].metadata).toEqual({
+          technologies: ['technology'],
+          targetGroups: {
+            group1: ['target1', 'target2'],
+            group2: ['target3'],
+          },
+        });
+      });
     });
 
     describe('source map', () => {
diff --git a/packages/nx/src/project-graph/utils/project-configuration-utils.ts b/packages/nx/src/project-graph/utils/project-configuration-utils.ts
index bb48f709c18fef..291e8fe93c1eff 100644
--- a/packages/nx/src/project-graph/utils/project-configuration-utils.ts
+++ b/packages/nx/src/project-graph/utils/project-configuration-utils.ts
@@ -252,7 +252,7 @@ export function mergeMetadata<T = ProjectMetadata | TargetMetadata>(
             }
           }
         } else {
-          result[metadataKey] = value;
+          result[metadataKey][key] = value[key];
           if (sourceMap) {
             sourceMap[`${baseSourceMapPath}.${metadataKey}`] =
               sourceInformation;