diff --git a/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java b/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
index 97da6ffc71b..0ff3f14a40f 100644
--- a/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
+++ b/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Repackager.java
@@ -20,7 +20,9 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 import java.util.jar.JarFile;
 import java.util.jar.Manifest;
@@ -154,29 +156,30 @@ public class Repackager {
 
 	private void repackage(JarFile sourceJar, File destination, Libraries libraries)
 			throws IOException {
-		final JarWriter writer = new JarWriter(destination);
+		JarWriter writer = new JarWriter(destination);
 		try {
-			final Set<String> seen = new HashSet<String>();
-			writer.writeManifest(buildManifest(sourceJar));
+			final List<Library> unpackLibraries = new ArrayList<Library>();
+			final List<Library> standardLibraries = new ArrayList<Library>();
+
 			libraries.doWithLibraries(new LibraryCallback() {
 				@Override
 				public void library(Library library) throws IOException {
 					File file = library.getFile();
 					if (isZip(file)) {
-						String destination = Repackager.this.layout
-								.getLibraryDestination(library.getName(),
-										library.getScope());
-						if (destination != null) {
-							if (!seen.add(destination + library.getName())) {
-								throw new IllegalStateException("Duplicate library "
-										+ library.getName());
-							}
-							writer.writeNestedLibrary(destination, library);
+						if (library.isUnpackRequired()) {
+							unpackLibraries.add(library);
+						}
+						else {
+							standardLibraries.add(library);
 						}
 					}
 				}
 			});
+			writer.writeManifest(buildManifest(sourceJar));
+			Set<String> seen = new HashSet<String>();
+			writeNestedLibraries(unpackLibraries, seen, writer);
 			writer.writeEntries(sourceJar);
+			writeNestedLibraries(standardLibraries, seen, writer);
 			if (this.layout.isExecutable()) {
 				writer.writeLoaderClasses();
 			}
@@ -191,6 +194,21 @@ public class Repackager {
 		}
 	}
 
+	private void writeNestedLibraries(List<Library> libraries, Set<String> alreadySeen,
+			JarWriter writer) throws IOException {
+		for (Library library : libraries) {
+			String destination = Repackager.this.layout.getLibraryDestination(
+					library.getName(), library.getScope());
+			if (destination != null) {
+				if (!alreadySeen.add(destination + library.getName())) {
+					throw new IllegalStateException("Duplicate library "
+							+ library.getName());
+				}
+				writer.writeNestedLibrary(destination, library);
+			}
+		}
+	}
+
 	private boolean isZip(File file) {
 		try {
 			FileInputStream fileInputStream = new FileInputStream(file);
diff --git a/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java b/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
index a8a92de05ea..8b3a91ad5d0 100644
--- a/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
+++ b/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java
@@ -32,6 +32,7 @@ import org.junit.rules.TemporaryFolder;
 import org.springframework.boot.loader.tools.sample.ClassWithMainMethod;
 import org.springframework.boot.loader.tools.sample.ClassWithoutMainMethod;
 import org.springframework.util.FileCopyUtils;
+import org.zeroturnaround.zip.ZipUtil;
 
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.startsWith;
@@ -393,6 +394,69 @@ public class RepackagerTests {
 		}
 	}
 
+	@Test
+	public void unpackLibrariesTakePrecedenceOverExistingSourceEntries() throws Exception {
+		final TestJarFile nested = new TestJarFile(this.temporaryFolder);
+		nested.addClass("a/b/C.class", ClassWithoutMainMethod.class);
+		final File nestedFile = nested.getFile();
+		this.testJarFile.addFile("lib/" + nestedFile.getName(), nested.getFile());
+		this.testJarFile.addClass("A.class", ClassWithMainMethod.class);
+		File file = this.testJarFile.getFile();
+		Repackager repackager = new Repackager(file);
+		repackager.repackage(new Libraries() {
+
+			@Override
+			public void doWithLibraries(LibraryCallback callback) throws IOException {
+				callback.library(new Library(nestedFile, LibraryScope.COMPILE, true));
+			}
+
+		});
+
+		JarFile jarFile = new JarFile(file);
+		try {
+			assertThat(jarFile.getEntry("lib/" + nestedFile.getName()).getComment(),
+					startsWith("UNPACK:"));
+		}
+		finally {
+			jarFile.close();
+		}
+	}
+
+	@Test
+	public void existingSourceEntriesTakePrecedenceOverStandardLibraries()
+			throws Exception {
+		final TestJarFile nested = new TestJarFile(this.temporaryFolder);
+		nested.addClass("a/b/C.class", ClassWithoutMainMethod.class);
+		final File nestedFile = nested.getFile();
+		this.testJarFile.addFile("lib/" + nestedFile.getName(), nested.getFile());
+		this.testJarFile.addClass("A.class", ClassWithMainMethod.class);
+		File file = this.testJarFile.getFile();
+		Repackager repackager = new Repackager(file);
+
+		long sourceLength = nestedFile.length();
+
+		repackager.repackage(new Libraries() {
+
+			@Override
+			public void doWithLibraries(LibraryCallback callback) throws IOException {
+				nestedFile.delete();
+				File toZip = RepackagerTests.this.temporaryFolder.newFile();
+				ZipUtil.packEntry(toZip, nestedFile);
+				callback.library(new Library(nestedFile, LibraryScope.COMPILE));
+			}
+
+		});
+
+		JarFile jarFile = new JarFile(file);
+		try {
+			assertThat(jarFile.getEntry("lib/" + nestedFile.getName()).getSize(),
+					equalTo(sourceLength));
+		}
+		finally {
+			jarFile.close();
+		}
+	}
+
 	private boolean hasLauncherClasses(File file) throws IOException {
 		return hasEntry(file, "org/springframework/boot/")
 				&& hasEntry(file, "org/springframework/boot/loader/JarLauncher.class");