diff --git a/src/utils/deconflictChunk.ts b/src/utils/deconflictChunk.ts
index 6f0d78c0667..e692d25f5d9 100644
--- a/src/utils/deconflictChunk.ts
+++ b/src/utils/deconflictChunk.ts
@@ -18,7 +18,7 @@ const DECONFLICT_IMPORTED_VARIABLES_BY_FORMAT: {
 	cjs: deconflictImportsOther,
 	es: deconflictImportsEsm,
 	iife: deconflictImportsOther,
-	system: deconflictImportsEsm,
+	system: deconflictImportsEsmOrSystem,
 	umd: deconflictImportsOther
 };
 
@@ -49,6 +49,29 @@ export function deconflictChunk(
 }
 
 function deconflictImportsEsm(
+	usedNames: Set<string>,
+	imports: Set<Variable>,
+	dependencies: Set<ExternalModule | Chunk>,
+	interop: boolean,
+	preserveModules: boolean
+) {
+	// Deconflict re-exported variables of dependencies when preserveModules is true.
+	// However, this implementation will result in unnecessary variable renaming without
+	// a deeper, wider fix.
+	//
+	// TODO: https://github.com/rollup/rollup/pull/3435#discussion_r390792792
+	if (preserveModules) {
+		for (const chunkOrExternalModule of dependencies) {
+			chunkOrExternalModule.variableName = getSafeName(
+				chunkOrExternalModule.variableName,
+				usedNames
+			);
+		}
+	}
+	deconflictImportsEsmOrSystem(usedNames, imports, dependencies, interop);
+}
+
+function deconflictImportsEsmOrSystem(
 	usedNames: Set<string>,
 	imports: Set<Variable>,
 	_dependencies: Set<ExternalModule | Chunk>,
diff --git a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/_external_commonjs-external b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/_external_commonjs-external
index 43be5de5e7e..daae6f0b371 100644
--- a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/_external_commonjs-external
+++ b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/_external_commonjs-external
@@ -1,5 +1,5 @@
-import external from 'external';
+import external$1 from 'external';
 
 
 
-export default external;
+export default external$1;
diff --git a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/other.js_commonjs-proxy b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/other.js_commonjs-proxy
index e1f8c6eb7c2..33c596f28e9 100644
--- a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/other.js_commonjs-proxy
+++ b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/_virtual/other.js_commonjs-proxy
@@ -1,5 +1,5 @@
-import { __moduleExports as other } from '../other.js';
+import { __moduleExports as other$1 } from '../other.js';
 
 
 
-export default other;
+export default other$1;
diff --git a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/commonjs.js b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/commonjs.js
index b78f6b0097e..583f1a12fdf 100644
--- a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/commonjs.js
+++ b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/commonjs.js
@@ -1,10 +1,10 @@
 import 'external';
-import external from './_virtual/_external_commonjs-external';
+import external$1 from './_virtual/_external_commonjs-external';
 import require$$0 from './_virtual/other.js_commonjs-proxy';
 
 const { value } = require$$0;
 
-console.log(external, value);
+console.log(external$1, value);
 
 var commonjs = 42;
 
diff --git a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/main.js b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/main.js
index bb1cdbb2d38..fbedb892d6c 100644
--- a/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/main.js
+++ b/test/chunking-form/samples/preserve-modules-commonjs/_expected/es/main.js
@@ -1,4 +1,4 @@
-import external from 'external';
+import external$1 from 'external';
 import value from './commonjs.js';
 
-console.log(value, external);
+console.log(value, external$1);
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_config.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_config.js
new file mode 100644
index 00000000000..650ae278b0d
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_config.js
@@ -0,0 +1,7 @@
+module.exports = {
+	description: 'confirm exports are deconflicted when exporting nested index aliases',
+	options: {
+		input: 'main.js',
+		preserveModules: true
+	}
+};
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/main.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/main.js
new file mode 100644
index 00000000000..12dccf71f8f
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/main.js
@@ -0,0 +1,10 @@
+define(['exports', './module-a/v1/index', './module-b/v1/index'], function (exports, index, index$1) { 'use strict';
+
+
+
+	exports.ModuleA_V1 = index;
+	exports.ModuleB_V1 = index$1;
+
+	Object.defineProperty(exports, '__esModule', { value: true });
+
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-a/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-a/v1/index.js
new file mode 100644
index 00000000000..2c1cbb5248d
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-a/v1/index.js
@@ -0,0 +1,9 @@
+define(['exports'], function (exports) { 'use strict';
+
+	const TEST_MODULE_A = 'A';
+
+	exports.TEST_MODULE_A = TEST_MODULE_A;
+
+	Object.defineProperty(exports, '__esModule', { value: true });
+
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-b/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-b/v1/index.js
new file mode 100644
index 00000000000..b56f633d9fb
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/amd/module-b/v1/index.js
@@ -0,0 +1,9 @@
+define(['exports'], function (exports) { 'use strict';
+
+	const TEST_MODULE_B = 'A';
+
+	exports.TEST_MODULE_B = TEST_MODULE_B;
+
+	Object.defineProperty(exports, '__esModule', { value: true });
+
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/main.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/main.js
new file mode 100644
index 00000000000..632ce47b9ae
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/main.js
@@ -0,0 +1,11 @@
+'use strict';
+
+Object.defineProperty(exports, '__esModule', { value: true });
+
+var index = require('./module-a/v1/index.js');
+var index$1 = require('./module-b/v1/index.js');
+
+
+
+exports.ModuleA_V1 = index;
+exports.ModuleB_V1 = index$1;
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-a/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-a/v1/index.js
new file mode 100644
index 00000000000..a8ab4802133
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-a/v1/index.js
@@ -0,0 +1,7 @@
+'use strict';
+
+Object.defineProperty(exports, '__esModule', { value: true });
+
+const TEST_MODULE_A = 'A';
+
+exports.TEST_MODULE_A = TEST_MODULE_A;
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-b/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-b/v1/index.js
new file mode 100644
index 00000000000..2c2b23c7d63
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/cjs/module-b/v1/index.js
@@ -0,0 +1,7 @@
+'use strict';
+
+Object.defineProperty(exports, '__esModule', { value: true });
+
+const TEST_MODULE_B = 'A';
+
+exports.TEST_MODULE_B = TEST_MODULE_B;
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/main.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/main.js
new file mode 100644
index 00000000000..537dda397a8
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/main.js
@@ -0,0 +1,4 @@
+import * as index from './module-a/v1/index.js';
+export { index as ModuleA_V1 };
+import * as index$1 from './module-b/v1/index.js';
+export { index$1 as ModuleB_V1 };
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-a/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-a/v1/index.js
new file mode 100644
index 00000000000..a8158380482
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-a/v1/index.js
@@ -0,0 +1,3 @@
+const TEST_MODULE_A = 'A';
+
+export { TEST_MODULE_A };
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-b/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-b/v1/index.js
new file mode 100644
index 00000000000..338a266e13c
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/es/module-b/v1/index.js
@@ -0,0 +1,3 @@
+const TEST_MODULE_B = 'A';
+
+export { TEST_MODULE_B };
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/main.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/main.js
new file mode 100644
index 00000000000..69423415aa6
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/main.js
@@ -0,0 +1,15 @@
+System.register(['./module-a/v1/index.js', './module-b/v1/index.js'], function (exports) {
+	'use strict';
+	return {
+		setters: [function (module) {
+			exports('ModuleA_V1', module);
+		}, function (module) {
+			exports('ModuleB_V1', module);
+		}],
+		execute: function () {
+
+
+
+		}
+	};
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-a/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-a/v1/index.js
new file mode 100644
index 00000000000..400a5460fc9
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-a/v1/index.js
@@ -0,0 +1,10 @@
+System.register([], function (exports) {
+	'use strict';
+	return {
+		execute: function () {
+
+			const TEST_MODULE_A = exports('TEST_MODULE_A', 'A');
+
+		}
+	};
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-b/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-b/v1/index.js
new file mode 100644
index 00000000000..337b556bb25
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/_expected/system/module-b/v1/index.js
@@ -0,0 +1,10 @@
+System.register([], function (exports) {
+	'use strict';
+	return {
+		execute: function () {
+
+			const TEST_MODULE_B = exports('TEST_MODULE_B', 'A');
+
+		}
+	};
+});
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/main.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/main.js
new file mode 100644
index 00000000000..6322b946820
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/main.js
@@ -0,0 +1,2 @@
+export * from './module-a/index'
+export * from './module-b/index'
\ No newline at end of file
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/index.js
new file mode 100644
index 00000000000..6bd359daf1f
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/index.js
@@ -0,0 +1,3 @@
+import * as ModuleA_V1 from './v1/index'
+
+export { ModuleA_V1 }
\ No newline at end of file
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/v1/index.js
new file mode 100644
index 00000000000..8bc392c756a
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-a/v1/index.js
@@ -0,0 +1 @@
+export const TEST_MODULE_A = 'A'
\ No newline at end of file
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/index.js
new file mode 100644
index 00000000000..f9b363cdf9f
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/index.js
@@ -0,0 +1,3 @@
+import * as ModuleB_V1 from './v1/index'
+
+export { ModuleB_V1 }
\ No newline at end of file
diff --git a/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/v1/index.js b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/v1/index.js
new file mode 100644
index 00000000000..1d751964f68
--- /dev/null
+++ b/test/chunking-form/samples/preserve-modules-nested-barrel-es-export/module-b/v1/index.js
@@ -0,0 +1 @@
+export const TEST_MODULE_B = 'A'
\ No newline at end of file
diff --git a/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/main.js b/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/main.js
index 0b42cf037c6..ae089cc4dae 100644
--- a/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/main.js
+++ b/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/main.js
@@ -1,4 +1,4 @@
-import { a } from './a.js';
+import { a as a$1 } from './a.js';
 import { d } from './one.js';
 
-console.log(a + d);
+console.log(a$1 + d);
diff --git a/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/one.js b/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/one.js
index d9291f1bff3..0d36a94fad2 100644
--- a/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/one.js
+++ b/test/chunking-form/samples/side-effect-free-dependencies/avoid-imports-preserve-modules/_expected/es/one.js
@@ -1,5 +1,5 @@
-import { b } from './b.js';
+import { b as b$1 } from './b.js';
 
-const d = b + 4;
+const d = b$1 + 4;
 
 export { d };
diff --git a/test/misc/bundle-information.js b/test/misc/bundle-information.js
index 70acf942b23..6a663b8d784 100644
--- a/test/misc/bundle-information.js
+++ b/test/misc/bundle-information.js
@@ -381,9 +381,9 @@ describe('The bundle object', () => {
 				assert.deepEqual(
 					output.map(chunk => chunk.code),
 					[
-						`import { other } from './other';
+						`import { other as other$1 } from './other';
 
-console.log(other);Promise.all([import('./dynamic1'), import('./dynamic2')]).then(([{dynamic1}, {dynamic2}]) => console.log(dynamic1, dynamic2));\n`,
+console.log(other$1);Promise.all([import('./dynamic1'), import('./dynamic2')]).then(([{dynamic1}, {dynamic2}]) => console.log(dynamic1, dynamic2));\n`,
 						'const dynamic1 = "dynamic1";\n\nexport { dynamic1 };\n',
 						'const other = "other";\n\nexport { other };\n',
 						'const dynamic2 = "dynamic2";\n\nexport { dynamic2 };\n'
@@ -418,7 +418,7 @@ console.log(other);Promise.all([import('./dynamic1'), import('./dynamic2')]).the
 								originalLength: 169,
 								removedExports: [],
 								renderedExports: [],
-								renderedLength: 141
+								renderedLength: 143
 							}
 						},
 						{