diff --git a/packages/nx/src/config/workspaces.spec.ts b/packages/nx/src/config/workspaces.spec.ts
index 4b1e66930a..6e1178d17d 100644
--- a/packages/nx/src/config/workspaces.spec.ts
+++ b/packages/nx/src/config/workspaces.spec.ts
@@ -79,13 +79,18 @@ describe('Workspaces', () => {
           }),
           'libs/domain/lib4/project.json': JSON.stringify(domainLibConfig),
           'libs/domain/lib4/package.json': JSON.stringify({}),
+          'workspace.json': JSON.stringify({
+            projects: { 'lib1-workspace': 'libs/lib1' },
+          }),
         },
         '/root'
       );
 
       const workspaces = new Workspaces('/root');
       const { projects } = workspaces.readWorkspaceConfiguration();
-      expect(projects.lib1).toEqual(lib1Config);
+      // projects got deduped so the workspace one remained
+      expect(projects['lib1-workspace']).toEqual(lib1Config);
+      expect(projects['lib1']).toBeUndefined();
       expect(projects.lib2).toEqual(lib2Config);
       expect(projects['domain-lib3']).toEqual(domainPackageConfig);
       expect(projects['domain-lib4']).toEqual(domainLibConfig);
diff --git a/packages/nx/src/config/workspaces.ts b/packages/nx/src/config/workspaces.ts
index fc5437447f..3eb828491a 100644
--- a/packages/nx/src/config/workspaces.ts
+++ b/packages/nx/src/config/workspaces.ts
@@ -86,10 +86,10 @@ export class Workspaces {
     const workspaceFile = workspaceConfigName(this.root);
 
     if (workspaceFile) {
-      workspace.projects = {
-        ...workspace.projects,
-        ...this.readFromWorkspaceJson().projects,
-      };
+      workspace.projects = this.mergeWorkspaceJsonAndGlobProjects(
+        this.readFromWorkspaceJson().projects,
+        workspace.projects
+      );
     }
 
     assertValidWorkspaceConfiguration(nxJson);
@@ -100,6 +100,24 @@ export class Workspaces {
     return this.cachedWorkspaceConfig;
   }
 
+  private mergeWorkspaceJsonAndGlobProjects(
+    workspaceJsonProjects: { [name: string]: any },
+    globProjects: { [name: string]: any }
+  ) {
+    const res = workspaceJsonProjects;
+    const folders = new Set();
+    for (let k of Object.keys(res)) {
+      folders.add(res[k].root);
+    }
+
+    for (let k of Object.keys(globProjects)) {
+      if (!folders.has(globProjects[k].root)) {
+        res[k] = globProjects[k];
+      }
+    }
+    return res;
+  }
+
   private mergeTargetDefaultsIntoProjectDescriptions(
     config: ProjectsConfigurations,
     nxJson: NxJsonConfiguration