diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
index 78ca1a712..3c7ae9bf9 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
@@ -57,12 +57,17 @@ import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.pgm.Command;
 import org.eclipse.jgit.pgm.TextBuiltin;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.kohsuke.args4j.Option;
 
 @Command(usage = "usage_RebuildRefTree")
 class RebuildRefTree extends TextBuiltin {
+	@Option(name = "--enable", usage = "set extensions.refsStorage = reftree")
+	boolean enable;
+
 	private String txnNamespace;
 	private String txnCommitted;
 
@@ -122,6 +127,15 @@ class RebuildRefTree extends TextBuiltin {
 			default:
 				throw die(String.format("%s: %s", update.getName(), result)); //$NON-NLS-1$
 			}
+
+			if (enable && !(db.getRefDatabase() instanceof RefTreeDatabase)) {
+				StoredConfig cfg = db.getConfig();
+				cfg.setInt("core", null, "repositoryformatversion", 1); //$NON-NLS-1$ //$NON-NLS-2$
+				cfg.setString("extensions", null, "refsStorage", "reftree"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+				cfg.save();
+				errw.println("Enabled reftree."); //$NON-NLS-1$
+				errw.flush();
+			}
 		}
 	}