diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index 63ca4289a..a6ea66bc0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -183,6 +183,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		}
 		Repository repository = null;
 		FetchResult fetchResult = null;
+		Thread cleanupHook = new Thread(() -> cleanup());
+		Runtime.getRuntime().addShutdownHook(cleanupHook);
 		try {
 			repository = init();
 			fetchResult = fetch(repository, u);
@@ -205,6 +207,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 			}
 			cleanup();
 			throw e;
+		} finally {
+			Runtime.getRuntime().removeShutdownHook(cleanupHook);
 		}
 		if (!noCheckout) {
 			try {