diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
index dd4487a30e..651be8294a 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
@@ -423,13 +423,14 @@ public class Repackager {
 			libraries.doWithLibraries((library) -> {
 				if (isZip(library.getFile())) {
 					String libraryDestination = Repackager.this.layout
-							.getLibraryDestination(library.getName(), library.getScope())
-							+ library.getName();
-					Library existing = this.libraryEntryNames
-							.putIfAbsent(libraryDestination, library);
-					if (existing != null) {
-						throw new IllegalStateException(
-								"Duplicate library " + library.getName());
+							.getLibraryDestination(library.getName(), library.getScope());
+					if (libraryDestination != null) {
+						Library existing = this.libraryEntryNames.putIfAbsent(
+								libraryDestination + library.getName(), library);
+						if (existing != null) {
+							throw new IllegalStateException(
+									"Duplicate library " + library.getName());
+						}
 					}
 				}
 			});
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
index e157f00d3d..52ad367edd 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
@@ -621,6 +621,23 @@ public class RepackagerTests {
 		assertThat(unpackLibrary.getComment()).startsWith("UNPACK:");
 	}
 
+	@Test
+	public void layoutCanOmitLibraries() throws IOException {
+		TestJarFile libJar = new TestJarFile(this.temporaryFolder);
+		libJar.addClass("a/b/C.class", ClassWithoutMainMethod.class);
+		final File libJarFile = libJar.getFile();
+		this.testJarFile.addClass("a/b/C.class", ClassWithMainMethod.class);
+		File file = this.testJarFile.getFile();
+		Repackager repackager = new Repackager(file);
+		Layout layout = mock(Layout.class);
+		final LibraryScope scope = mock(LibraryScope.class);
+		repackager.setLayout(layout);
+		repackager.repackage(
+				(callback) -> callback.library(new Library(libJarFile, scope)));
+		assertThat(getEntryNames(file)).containsExactly("META-INF/",
+				"META-INF/MANIFEST.MF", "a/", "a/b/", "a/b/C.class");
+	}
+
 	private File createLibrary() throws IOException {
 		TestJarFile library = new TestJarFile(this.temporaryFolder);
 		library.addClass("com/example/library/Library.class",