diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index 0d7009dca..0ad067f6a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -370,8 +370,7 @@ public class CloneCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCloneRepositoryOnlyOneBranch() throws IOException,
-			JGitInternalException, GitAPIException {
+	public void testCloneRepositoryOnlyOneBranch() throws Exception {
 		File directory = createTempDirectory("testCloneRepositoryWithBranch");
 		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
@@ -385,22 +384,40 @@ public class CloneCommandTest extends RepositoryTestCase {
 		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/master");
 		assertEquals("refs/remotes/origin/master", allRefNames(git2
 				.branchList().setListMode(ListMode.REMOTE).call()));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(
+				new RefSpec("+refs/heads/master:refs/remotes/origin/master"),
+				specs.get(0));
+	}
 
+	@Test
+	public void testBareCloneRepositoryOnlyOneBranch() throws Exception {
 		// Same thing, but now test with bare repo
-		directory = createTempDirectory("testCloneRepositoryWithBranch_bare");
-		command = Git.cloneRepository();
+		File directory = createTempDirectory(
+				"testCloneRepositoryWithBranch_bare");
+		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
 		command.setBranchesToClone(Collections
 				.singletonList("refs/heads/master"));
 		command.setDirectory(directory);
 		command.setURI(fileUri());
 		command.setBare(true);
-		git2 = command.call();
+		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertNotNull(git2);
 		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/master");
 		assertEquals("refs/heads/master", allRefNames(git2.branchList()
 				.setListMode(ListMode.ALL).call()));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(
+				new RefSpec("+refs/heads/master:refs/heads/master"),
+				specs.get(0));
 	}
 
 	public static String allRefNames(List<Ref> refs) {
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 5c06bac1f..5ea7cf871 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -284,11 +284,9 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 
 		final String dst = (bare ? Constants.R_HEADS : Constants.R_REMOTES
 				+ config.getName() + "/") + "*"; //$NON-NLS-1$//$NON-NLS-2$
-		RefSpec refSpec = new RefSpec();
-		refSpec = refSpec.setForceUpdate(true);
-		refSpec = refSpec.setSourceDestination(Constants.R_HEADS + "*", dst); //$NON-NLS-1$
+		List<RefSpec> refSpecs = calculateRefSpecs(dst);
 
-		config.addFetchRefSpec(refSpec);
+		config.setFetchRefSpecs(refSpecs);
 		config.update(clonedRepo.getConfig());
 
 		clonedRepo.getConfig().save();
@@ -300,9 +298,6 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		command.setTagOpt(TagOpt.FETCH_TAGS);
 		configure(command);
 
-		List<RefSpec> specs = calculateRefSpecs(dst);
-		command.setRefSpecs(specs);
-
 		return command.call();
 	}
 
@@ -311,13 +306,15 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		wcrs = wcrs.setForceUpdate(true);
 		wcrs = wcrs.setSourceDestination(Constants.R_HEADS + "*", dst); //$NON-NLS-1$
 		List<RefSpec> specs = new ArrayList<>();
-		if (cloneAllBranches)
-			specs.add(wcrs);
-		else if (branchesToClone != null
-				&& branchesToClone.size() > 0) {
-			for (String selectedRef : branchesToClone)
-				if (wcrs.matchSource(selectedRef))
+		if (!cloneAllBranches && branchesToClone != null
+				&& !branchesToClone.isEmpty()) {
+			for (String selectedRef : branchesToClone) {
+				if (wcrs.matchSource(selectedRef)) {
 					specs.add(wcrs.expandFromSource(selectedRef));
+				}
+			}
+		} else {
+			specs.add(wcrs);
 		}
 		return specs;
 	}