diff --git a/packages/workspace/src/generators/move/lib/update-imports.spec.ts b/packages/workspace/src/generators/move/lib/update-imports.spec.ts
index 09b8c6f256fc1..1ec416eec5d05 100644
--- a/packages/workspace/src/generators/move/lib/update-imports.spec.ts
+++ b/packages/workspace/src/generators/move/lib/update-imports.spec.ts
@@ -1,12 +1,13 @@
 import { readJson, readProjectConfiguration, Tree } from '@nrwl/devkit';
 import { createTreeWithEmptyV1Workspace } from '@nrwl/devkit/testing';
 import { libraryGenerator } from '../../library/library';
-import { NormalizedSchema } from '../schema';
+import { Schema } from '../schema';
 import { updateImports } from './update-imports';
+import { normalizeSchema } from './normalize-schema';
 
 describe('updateImports', () => {
   let tree: Tree;
-  let schema: NormalizedSchema;
+  let schema: Schema;
 
   beforeEach(async () => {
     tree = createTreeWithEmptyV1Workspace();
@@ -14,10 +15,7 @@ describe('updateImports', () => {
     schema = {
       projectName: 'my-source',
       destination: 'my-destination',
-      importPath: '@proj/my-destination',
       updateImportPath: true,
-      newProjectName: 'my-destination',
-      relativeToRootDestination: 'libs/my-destination',
     };
   });
 
@@ -48,7 +46,11 @@ describe('updateImports', () => {
     );
     const projectConfig = readProjectConfiguration(tree, 'my-source');
 
-    updateImports(tree, schema, projectConfig);
+    updateImports(
+      tree,
+      normalizeSchema(tree, schema, projectConfig),
+      projectConfig
+    );
 
     expect(tree.read(importerFilePath, 'utf-8')).toMatchSnapshot();
   });
@@ -261,7 +263,18 @@ export MyExtendedClass extends MyClass {};`
     schema.updateImportPath = false;
     const projectConfig = readProjectConfiguration(tree, 'my-source');
 
-    updateImports(tree, { ...schema, updateImportPath: false }, projectConfig);
+    updateImports(
+      tree,
+      normalizeSchema(
+        tree,
+        {
+          ...schema,
+          updateImportPath: false,
+        },
+        projectConfig
+      ),
+      projectConfig
+    );
 
     expect(tree.read(importerFilePath).toString()).toContain(
       `import { MyClass } from '@proj/my-source';`
@@ -275,7 +288,11 @@ export MyExtendedClass extends MyClass {};`
     });
     const projectConfig = readProjectConfiguration(tree, 'my-source');
 
-    updateImports(tree, schema, projectConfig);
+    updateImports(
+      tree,
+      normalizeSchema(tree, schema, projectConfig),
+      projectConfig
+    );
 
     const tsConfig = readJson(tree, '/tsconfig.base.json');
     expect(tsConfig.compilerOptions.paths).toEqual({
@@ -283,6 +300,26 @@ export MyExtendedClass extends MyClass {};`
     });
   });
 
+  it('should update project ref of a project not under libs in the root tsconfig.base.json', async () => {
+    tree.delete('libs');
+    await libraryGenerator(tree, {
+      name: 'my-source',
+      standaloneConfig: false,
+    });
+    const projectConfig = readProjectConfiguration(tree, 'my-source');
+
+    updateImports(
+      tree,
+      normalizeSchema(tree, schema, projectConfig),
+      projectConfig
+    );
+
+    const tsConfig = readJson(tree, '/tsconfig.base.json');
+    expect(tsConfig.compilerOptions.paths).toEqual({
+      '@proj/my-destination': ['my-destination/src/index.ts'],
+    });
+  });
+
   it('should update project ref in the root tsconfig.json when no tsconfig.base.json', async () => {
     tree.rename('tsconfig.base.json', 'tsconfig.json');
     await libraryGenerator(tree, {
@@ -291,7 +328,11 @@ export MyExtendedClass extends MyClass {};`
     });
     const projectConfig = readProjectConfiguration(tree, 'my-source');
 
-    updateImports(tree, schema, projectConfig);
+    updateImports(
+      tree,
+      normalizeSchema(tree, schema, projectConfig),
+      projectConfig
+    );
 
     const tsConfig = readJson(tree, '/tsconfig.json');
     expect(tsConfig.compilerOptions.paths).toEqual({
@@ -306,7 +347,19 @@ export MyExtendedClass extends MyClass {};`
     });
     const projectConfig = readProjectConfiguration(tree, 'my-source');
 
-    updateImports(tree, { ...schema, updateImportPath: false }, projectConfig);
+    updateImports(
+      tree,
+      normalizeSchema(
+        tree,
+        {
+          ...schema,
+          updateImportPath: false,
+        },
+        projectConfig
+      ),
+
+      projectConfig
+    );
 
     const tsConfig = readJson(tree, '/tsconfig.base.json');
     expect(tsConfig.compilerOptions.paths).toEqual({
diff --git a/packages/workspace/src/generators/move/lib/update-imports.ts b/packages/workspace/src/generators/move/lib/update-imports.ts
index c4ba29ffa4479..eb935048ef082 100644
--- a/packages/workspace/src/generators/move/lib/update-imports.ts
+++ b/packages/workspace/src/generators/move/lib/update-imports.ts
@@ -3,6 +3,7 @@ import {
   ChangeType,
   getProjects,
   getWorkspaceLayout,
+  joinPathFragments,
   ProjectConfiguration,
   StringChange,
   Tree,
@@ -15,6 +16,7 @@ import { getRootTsConfigPathInTree } from '../../../utilities/typescript';
 import { findNodes } from 'nx/src/utils/typescript';
 import { NormalizedSchema } from '../schema';
 import { normalizeSlashes } from './utils';
+import { relative } from 'path';
 
 /**
  * Updates all the imports in the workspace and modifies the tsconfig appropriately.
@@ -81,8 +83,8 @@ export function updateImports(
   }
 
   const projectRoot = {
-    from: project.root.slice(libsDir.length).replace(/^\/|\\/, ''),
-    to: schema.destination,
+    from: project.root,
+    to: schema.relativeToRootDestination,
   };
 
   if (tsConfig) {
@@ -96,7 +98,7 @@ export function updateImports(
       );
     }
     const updatedPath = path.map((x) =>
-      x.replace(new RegExp(projectRoot.from, 'g'), projectRoot.to)
+      joinPathFragments(projectRoot.to, relative(projectRoot.from, x))
     );
 
     if (schema.updateImportPath) {
diff --git a/packages/workspace/src/generators/remove/lib/update-tsconfig.spec.ts b/packages/workspace/src/generators/remove/lib/update-tsconfig.spec.ts
index b71b4721143ee..d74e8930ffbfc 100644
--- a/packages/workspace/src/generators/remove/lib/update-tsconfig.spec.ts
+++ b/packages/workspace/src/generators/remove/lib/update-tsconfig.spec.ts
@@ -1,16 +1,28 @@
-import { readJson, readProjectConfiguration, Tree } from '@nrwl/devkit';
-import { createTreeWithEmptyV1Workspace } from '@nrwl/devkit/testing';
+import {
+  ProjectGraph,
+  readJson,
+  readProjectConfiguration,
+  Tree,
+} from '@nrwl/devkit';
+import { createTreeWithEmptyWorkspace } from '@nrwl/devkit/testing';
 import { Schema } from '../schema';
 import { updateTsconfig } from './update-tsconfig';
 import { libraryGenerator } from '../../library/library';
 
+let graph: ProjectGraph;
+jest.mock('@nrwl/devkit', () => {
+  return {
+    ...jest.requireActual('@nrwl/devkit'),
+    createProjectGraphAsync: jest.fn().mockImplementation(() => graph),
+  };
+});
 describe('updateTsconfig', () => {
   let tree: Tree;
   let schema: Schema;
   let schemaWithImportPath: Schema;
 
   beforeEach(async () => {
-    tree = createTreeWithEmptyV1Workspace();
+    tree = createTreeWithEmptyWorkspace();
 
     schema = {
       projectName: 'my-lib',
@@ -31,9 +43,47 @@ describe('updateTsconfig', () => {
       name: 'my-lib',
       standaloneConfig: false,
     });
-    const project = readProjectConfiguration(tree, 'my-lib');
 
-    updateTsconfig(tree, schema, project);
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schema);
+
+    const tsConfig = readJson(tree, '/tsconfig.base.json');
+    expect(tsConfig.compilerOptions.paths).toEqual({});
+  });
+
+  it('should delete project ref not under libs from the root tsconfig.base.json', async () => {
+    tree.delete('libs');
+    await libraryGenerator(tree, {
+      name: 'my-lib',
+      standaloneConfig: false,
+    });
+
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schema);
 
     const tsConfig = readJson(tree, '/tsconfig.base.json');
     expect(tsConfig.compilerOptions.paths).toEqual({});
@@ -45,9 +95,21 @@ describe('updateTsconfig', () => {
       standaloneConfig: false,
       importPath: '@proj/whatever-name',
     });
-    const project = readProjectConfiguration(tree, 'my-lib');
 
-    updateTsconfig(tree, schemaWithImportPath, project);
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schemaWithImportPath);
 
     const tsConfig = readJson(tree, '/tsconfig.base.json');
     expect(tsConfig.compilerOptions.paths).toEqual({});
@@ -59,9 +121,21 @@ describe('updateTsconfig', () => {
       name: 'my-lib',
       standaloneConfig: false,
     });
-    const project = readProjectConfiguration(tree, 'my-lib');
 
-    updateTsconfig(tree, schema, project);
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schema);
 
     const tsConfig = readJson(tree, '/tsconfig.json');
     expect(tsConfig.compilerOptions.paths).toEqual({});
@@ -74,11 +148,64 @@ describe('updateTsconfig', () => {
       standaloneConfig: false,
       importPath: '@proj/whatever-name',
     });
-    const project = readProjectConfiguration(tree, 'my-lib');
 
-    updateTsconfig(tree, schemaWithImportPath, project);
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schemaWithImportPath);
 
     const tsConfig = readJson(tree, '/tsconfig.json');
     expect(tsConfig.compilerOptions.paths).toEqual({});
   });
+
+  it('should not delete importPaths of nested projects from tsconfig.base.json', async () => {
+    await libraryGenerator(tree, {
+      name: 'my-lib',
+      standaloneConfig: false,
+      importPath: '@proj/whatever-name',
+    });
+    await libraryGenerator(tree, {
+      name: 'nested-lib',
+      directory: 'libs/my-lib',
+      standaloneConfig: false,
+      importPath: '@proj/nested/whatever-name',
+    });
+
+    graph = {
+      nodes: {
+        'my-lib': {
+          name: 'my-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib').root,
+          },
+        },
+        'my-lib-nested-lib': {
+          name: 'my-lib-nested-lib',
+          type: 'lib',
+          data: {
+            root: readProjectConfiguration(tree, 'my-lib-nested-lib').root,
+          },
+        },
+      },
+      dependencies: {},
+    };
+
+    await updateTsconfig(tree, schemaWithImportPath);
+
+    const tsConfig = readJson(tree, '/tsconfig.base.json');
+    expect(tsConfig.compilerOptions.paths).toEqual({
+      '@proj/nested/whatever-name': ['libs/my-lib/nested-lib/src/index.ts'],
+    });
+  });
 });
diff --git a/packages/workspace/src/generators/remove/lib/update-tsconfig.ts b/packages/workspace/src/generators/remove/lib/update-tsconfig.ts
index a5a2c633b6e63..1d3e16c0086b7 100644
--- a/packages/workspace/src/generators/remove/lib/update-tsconfig.ts
+++ b/packages/workspace/src/generators/remove/lib/update-tsconfig.ts
@@ -1,38 +1,41 @@
 import {
-  getWorkspaceLayout,
-  ProjectConfiguration,
+  createProjectGraphAsync,
+  normalizePath,
+  ProjectGraph,
   Tree,
   updateJson,
 } from '@nrwl/devkit';
-import { getImportPath } from 'nx/src/utils/path';
 import { getRootTsConfigPathInTree } from '../../../utilities/typescript';
 import { Schema } from '../schema';
+import {
+  createProjectRootMappings,
+  findProjectForPath,
+} from 'nx/src/project-graph/utils/find-project-for-path';
 
 /**
  * Updates the tsconfig paths to remove the project.
  *
  * @param schema The options provided to the schematic
  */
-export function updateTsconfig(
-  tree: Tree,
-  schema: Schema,
-  project: ProjectConfiguration
-) {
-  const { appsDir, libsDir, npmScope } = getWorkspaceLayout(tree);
-
+export async function updateTsconfig(tree: Tree, schema: Schema) {
   const tsConfigPath = getRootTsConfigPathInTree(tree);
-  const defaultImportPath = getImportPath(
-    npmScope,
-    project.root
-      .slice(
-        project.projectType === 'application' ? appsDir.length : libsDir.length
-      )
-      .replace(/^\/|\\/, '')
-  );
-  const importPath = schema.importPath || defaultImportPath;
+
   if (tree.exists(tsConfigPath)) {
+    const graph: ProjectGraph = await createProjectGraphAsync();
+    const projectMapping = createProjectRootMappings(graph.nodes);
     updateJson(tree, tsConfigPath, (json) => {
-      delete json.compilerOptions.paths[importPath];
+      for (const importPath in json.compilerOptions.paths) {
+        for (const path of json.compilerOptions.paths[importPath]) {
+          const project = findProjectForPath(
+            normalizePath(path),
+            projectMapping
+          );
+          if (project === schema.projectName) {
+            delete json.compilerOptions.paths[importPath];
+            break;
+          }
+        }
+      }
       return json;
     });
   }
diff --git a/packages/workspace/src/generators/remove/remove.ts b/packages/workspace/src/generators/remove/remove.ts
index 54b24bbc112ee..6d77c8d128f7b 100644
--- a/packages/workspace/src/generators/remove/remove.ts
+++ b/packages/workspace/src/generators/remove/remove.ts
@@ -1,6 +1,8 @@
 import {
   convertNxGenerator,
+  createProjectGraphAsync,
   formatFiles,
+  ProjectGraph,
   readProjectConfiguration,
   Tree,
 } from '@nrwl/devkit';
@@ -20,7 +22,7 @@ export async function removeGenerator(tree: Tree, schema: Schema) {
   updateJestConfig(tree, schema, project);
   removeProjectConfig(tree, schema);
   removeProject(tree, project);
-  updateTsconfig(tree, schema, project);
+  await updateTsconfig(tree, schema);
   if (!schema.skipFormat) {
     await formatFiles(tree);
   }