diff --git a/src/ast/nodes/Program.ts b/src/ast/nodes/Program.ts
index 9a23794c60c..e82cc2bf2b6 100644
--- a/src/ast/nodes/Program.ts
+++ b/src/ast/nodes/Program.ts
@@ -18,6 +18,9 @@ export default class Program extends NodeBase {
 	private hasLoggedEffect = false;
 
 	hasCachedEffects(): boolean {
+		if (!this.included) {
+			return false;
+		}
 		return this.hasCachedEffect === null
 			? (this.hasCachedEffect = this.hasEffects(createHasEffectsContext()))
 			: this.hasCachedEffect;
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_config.js b/test/chunking-form/samples/manual-chunk-not-included/_config.js
new file mode 100644
index 00000000000..4ad3e9f1e3a
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_config.js
@@ -0,0 +1,11 @@
+module.exports = {
+	description: 'handles manual chunks where the root is not part of the module graph',
+	options: {
+		input: ['main.js'],
+		output: {
+			manualChunks: {
+				manual: ['manual-entry.js']
+			}
+		}
+	}
+};
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/generated-manual.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/generated-manual.js
new file mode 100644
index 00000000000..f9e8bf57b21
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/generated-manual.js
@@ -0,0 +1,5 @@
+define((function () { 'use strict';
+
+	console.log('included');
+
+}));
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/main.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/main.js
new file mode 100644
index 00000000000..b9a9d643047
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/amd/main.js
@@ -0,0 +1,5 @@
+define(['./generated-manual'], (function (manual) { 'use strict';
+
+	console.log('main');
+
+}));
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/generated-manual.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/generated-manual.js
new file mode 100644
index 00000000000..46970f369e4
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/generated-manual.js
@@ -0,0 +1,3 @@
+'use strict';
+
+console.log('included');
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/main.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/main.js
new file mode 100644
index 00000000000..f679e51bff2
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/cjs/main.js
@@ -0,0 +1,5 @@
+'use strict';
+
+require('./generated-manual.js');
+
+console.log('main');
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/es/generated-manual.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/es/generated-manual.js
new file mode 100644
index 00000000000..452029d8355
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/es/generated-manual.js
@@ -0,0 +1 @@
+console.log('included');
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/es/main.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/es/main.js
new file mode 100644
index 00000000000..ddeb648f149
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/es/main.js
@@ -0,0 +1,3 @@
+import './generated-manual.js';
+
+console.log('main');
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/system/generated-manual.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/system/generated-manual.js
new file mode 100644
index 00000000000..f147b38fa45
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/system/generated-manual.js
@@ -0,0 +1,10 @@
+System.register([], (function () {
+	'use strict';
+	return {
+		execute: (function () {
+
+			console.log('included');
+
+		})
+	};
+}));
diff --git a/test/chunking-form/samples/manual-chunk-not-included/_expected/system/main.js b/test/chunking-form/samples/manual-chunk-not-included/_expected/system/main.js
new file mode 100644
index 00000000000..3e762e61fd8
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/_expected/system/main.js
@@ -0,0 +1,11 @@
+System.register(['./generated-manual.js'], (function () {
+	'use strict';
+	return {
+		setters: [null],
+		execute: (function () {
+
+			console.log('main');
+
+		})
+	};
+}));
diff --git a/test/chunking-form/samples/manual-chunk-not-included/main.js b/test/chunking-form/samples/manual-chunk-not-included/main.js
new file mode 100644
index 00000000000..8e6e9e0b963
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/main.js
@@ -0,0 +1,2 @@
+import './manual-included';
+console.log('main');
diff --git a/test/chunking-form/samples/manual-chunk-not-included/manual-entry.js b/test/chunking-form/samples/manual-chunk-not-included/manual-entry.js
new file mode 100644
index 00000000000..9947c39b198
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/manual-entry.js
@@ -0,0 +1,5 @@
+import './manual-included';
+
+function test() {}
+
+test();
diff --git a/test/chunking-form/samples/manual-chunk-not-included/manual-included.js b/test/chunking-form/samples/manual-chunk-not-included/manual-included.js
new file mode 100644
index 00000000000..452029d8355
--- /dev/null
+++ b/test/chunking-form/samples/manual-chunk-not-included/manual-included.js
@@ -0,0 +1 @@
+console.log('included');