diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
index 8fce30a2a..c9aaa3994 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -649,6 +649,7 @@ truncatedHunkOldLinesMissing=Truncated hunk, at least {0} old lines is missing
 tSizeMustBeGreaterOrEqual1=tSize must be >= 1
 unableToCheckConnectivity=Unable to check connectivity.
 unableToCreateNewObject=Unable to create new object: {0}
+unableToRemovePath=Unable to remove path ''{0}''
 unableToStore=Unable to store {0}.
 unableToWrite=Unable to write {0}
 unauthorized=Unauthorized
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
index a4a970e24..a8dfc2d2a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -708,6 +708,7 @@ public static JGitText get() {
 	/***/ public String tSizeMustBeGreaterOrEqual1;
 	/***/ public String unableToCheckConnectivity;
 	/***/ public String unableToCreateNewObject;
+	/***/ public String unableToRemovePath;
 	/***/ public String unableToStore;
 	/***/ public String unableToWrite;
 	/***/ public String unauthorized;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 48fdf8119..8338b2c8a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -63,6 +63,7 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.DirectoryNotEmptyException;
 import java.nio.file.Files;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
@@ -1092,9 +1093,14 @@ private static void delete(final File file, final int depth, LockFile rLck)
 		File dir = file.getParentFile();
 		for (int i = 0; i < depth; ++i) {
 			try {
-				Files.delete(dir.toPath());
+				Files.deleteIfExists(dir.toPath());
+			} catch (DirectoryNotEmptyException e) {
+				// Don't log; normal case when there are other refs with the
+				// same prefix
+				break;
 			} catch (IOException e) {
-				LOG.warn("Unable to remove path {}", dir, e);
+				LOG.warn(MessageFormat.format(JGitText.get().unableToRemovePath,
+						dir), e);
 				break;
 			}
 			dir = dir.getParentFile();