diff --git a/packages/compiler-cli/src/ngtsc/entry_point/src/generator.ts b/packages/compiler-cli/src/ngtsc/entry_point/src/generator.ts
index cb01e6a60f..ef1eaa614a 100644
--- a/packages/compiler-cli/src/ngtsc/entry_point/src/generator.ts
+++ b/packages/compiler-cli/src/ngtsc/entry_point/src/generator.ts
@@ -12,6 +12,7 @@ import * as path from 'path';
 import * as ts from 'typescript';
 
 import {ShimGenerator} from '../../shims';
+import {relativePathBetween} from '../../util/src/path';
 
 export class FlatIndexGenerator implements ShimGenerator {
   readonly flatIndexPath: string;
@@ -27,10 +28,7 @@ export class FlatIndexGenerator implements ShimGenerator {
   recognize(fileName: string): boolean { return fileName === this.flatIndexPath; }
 
   generate(): ts.SourceFile {
-    const relativeEntryPoint = './' +
-        path.posix.relative(path.posix.dirname(this.flatIndexPath), this.entryPoint)
-            .replace(/\.tsx?$/, '');
-
+    const relativeEntryPoint = relativePathBetween(this.flatIndexPath, this.entryPoint);
     const contents = `/**
  * Generated bundle index. Do not edit.
  */
diff --git a/packages/compiler-cli/src/ngtsc/entry_point/src/logic.ts b/packages/compiler-cli/src/ngtsc/entry_point/src/logic.ts
index de233eda36..5bfa55d56b 100644
--- a/packages/compiler-cli/src/ngtsc/entry_point/src/logic.ts
+++ b/packages/compiler-cli/src/ngtsc/entry_point/src/logic.ts
@@ -6,6 +6,7 @@
  * found in the LICENSE file at https://angular.io/license
  */
 
+import {normalizeSeparators} from '../../util/src/path';
 import {isNonDeclarationTsPath} from '../../util/src/typescript';
 
 export function findFlatIndexEntryPoint(rootFiles: ReadonlyArray<string>): string|null {
@@ -13,22 +14,24 @@ export function findFlatIndexEntryPoint(rootFiles: ReadonlyArray<string>): strin
   // 1) if it's the only file!!!!!!
   // 2) (deprecated) if it's named 'index.ts' and has the shortest path of all such files.
   const tsFiles = rootFiles.filter(file => isNonDeclarationTsPath(file));
+  let resolvedEntryPoint: string|null = null;
+
   if (tsFiles.length === 1) {
     // There's only one file - this is the flat module index.
-    return tsFiles[0];
+    resolvedEntryPoint = tsFiles[0];
   } else {
     // In the event there's more than one TS file, one of them can still be selected as the
     // flat module index if it's named 'index.ts'. If there's more than one 'index.ts', the one
     // with the shortest path wins.
     //
     // This behavior is DEPRECATED and only exists to support existing usages.
-    let indexFile: string|null = null;
     for (const tsFile of tsFiles) {
       if (tsFile.endsWith('/index.ts') &&
-          (indexFile === null || tsFile.length <= indexFile.length)) {
-        indexFile = tsFile;
+          (resolvedEntryPoint === null || tsFile.length <= resolvedEntryPoint.length)) {
+        resolvedEntryPoint = tsFile;
       }
     }
-    return indexFile;
   }
+
+  return resolvedEntryPoint ? normalizeSeparators(resolvedEntryPoint) : null;
 }
diff --git a/packages/compiler-cli/src/ngtsc/entry_point/test/entry_point_spec.ts b/packages/compiler-cli/src/ngtsc/entry_point/test/entry_point_spec.ts
new file mode 100644
index 0000000000..0c2931fd19
--- /dev/null
+++ b/packages/compiler-cli/src/ngtsc/entry_point/test/entry_point_spec.ts
@@ -0,0 +1,28 @@
+
+/**
+ * @license
+ * Copyright Google Inc. All Rights Reserved.
+ *
+ * Use of this source code is governed by an MIT-style license that can be
+ * found in the LICENSE file at https://angular.io/license
+ */
+
+import {findFlatIndexEntryPoint} from '../src/logic';
+
+describe('entry_point logic', () => {
+
+  describe('findFlatIndexEntryPoint', () => {
+
+    it('should use the only source file if only a single one is specified',
+       () => { expect(findFlatIndexEntryPoint(['/src/index.ts'])).toBe('/src/index.ts'); });
+
+    it('should use the shortest source file ending with "index.ts" for multiple files', () => {
+      expect(findFlatIndexEntryPoint([
+        '/src/deep/index.ts', '/src/index.ts', '/index.ts'
+      ])).toBe('/index.ts');
+    });
+
+    it('should normalize the path separators for the found entry point',
+       () => { expect(findFlatIndexEntryPoint(['\\src\\index.ts'])).toBe('/src/index.ts'); });
+  });
+});
diff --git a/packages/compiler-cli/src/ngtsc/program.ts b/packages/compiler-cli/src/ngtsc/program.ts
index 7cdb18d0cd..30926d17aa 100644
--- a/packages/compiler-cli/src/ngtsc/program.ts
+++ b/packages/compiler-cli/src/ngtsc/program.ts
@@ -24,6 +24,7 @@ import {FactoryGenerator, FactoryInfo, GeneratedShimsHostWrapper, ShimGenerator,
 import {ivySwitchTransform} from './switch';
 import {IvyCompilation, ivyTransformFactory} from './transform';
 import {TypeCheckContext, TypeCheckProgramHost} from './typecheck';
+import {normalizeSeparators} from './util/src/path';
 import {isDtsPath} from './util/src/typescript';
 
 export class NgtscProgram implements api.Program {
@@ -107,8 +108,9 @@ export class NgtscProgram implements api.Program {
         });
       } else {
         const flatModuleId = options.flatModuleId || null;
+        const flatModuleOutFile = normalizeSeparators(options.flatModuleOutFile);
         this.flatIndexGenerator =
-            new FlatIndexGenerator(entryPoint, options.flatModuleOutFile, flatModuleId);
+            new FlatIndexGenerator(entryPoint, flatModuleOutFile, flatModuleId);
         generators.push(this.flatIndexGenerator);
         rootFiles.push(this.flatIndexGenerator.flatIndexPath);
       }
diff --git a/packages/compiler-cli/test/ngtsc/ngtsc_spec.ts b/packages/compiler-cli/test/ngtsc/ngtsc_spec.ts
index befe6e253a..cff67d3790 100644
--- a/packages/compiler-cli/test/ngtsc/ngtsc_spec.ts
+++ b/packages/compiler-cli/test/ngtsc/ngtsc_spec.ts
@@ -1610,6 +1610,17 @@ describe('ngtsc behavioral tests', () => {
       expect(dtsContents).toContain('/// <amd-module name="@mymodule" />');
     });
 
+    it('should generate a proper flat module index file when nested', () => {
+      env.tsconfig({
+        'flatModuleOutFile': './public-api/index.js',
+      });
+
+      env.write('test.ts', `export const SOME_EXPORT = 'some-export'`);
+      env.driveMain();
+
+      expect(env.getContents('./public-api/index.js')).toContain(`export * from '../test';`);
+    });
+
     it('should report an error when a flat module index is requested but no entrypoint can be determined',
        () => {
          env.tsconfig({'flatModuleOutFile': 'flat.js'});