diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableStackTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableStackTest.java
index 6c74f0079..98e4b3e1b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableStackTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableStackTest.java
@@ -14,6 +14,7 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThrows;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assume.assumeFalse;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -32,10 +33,12 @@
 import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
+
 public class FileReftableStackTest {
 
 	private static Ref newRef(String name, ObjectId id) {
@@ -118,6 +121,9 @@ public void testCompaction1024() throws Exception {
 	@SuppressWarnings({ "resource", "unused" })
 	@Test
 	public void missingReftable() throws Exception {
+		// Can't delete in-use files on Windows.
+		assumeFalse(SystemReader.getInstance().isWindows());
+
 		try (FileReftableStack stack = new FileReftableStack(
 				new File(reftableDir, "refs"), reftableDir, null,
 				() -> new Config())) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
index f02c8613a..5152367d2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
@@ -40,6 +40,7 @@
 import org.eclipse.jgit.internal.storage.reftable.ReftableWriter;
 import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.SystemReader;
 
 /**
  * A mutable stack of reftables on local filesystem storage. Not thread-safe.
@@ -527,11 +528,19 @@ boolean compactRange(int first, int last) throws IOException {
 				return false;
 			}
 
+			reload();
 			for (File f : deleteOnSuccess) {
-				Files.delete(f.toPath());
+				try {
+					Files.delete(f.toPath());
+				} catch (IOException e) {
+					// Ignore: this can happen on Windows in case of concurrent processes.
+					// leave the garbage and continue.
+					if (!SystemReader.getInstance().isWindows()) {
+						throw e;
+					}
+				}
 			}
 
-			reload();
 			return true;
 		} finally {
 			if (tmpTable != null) {