diff --git a/refs.c b/refs.c
index 388ac3ed35..1e762fb8bc 100644
--- a/refs.c
+++ b/refs.c
@@ -4093,9 +4093,19 @@ cleanup:
 	return ret;
 }
 
+static int ref_present(const char *refname,
+		       const struct object_id *oid, int flags, void *cb_data)
+{
+	struct string_list *affected_refnames = cb_data;
+
+	return string_list_has_string(affected_refnames, refname);
+}
+
 int initial_ref_transaction_commit(struct ref_transaction *transaction,
 				   struct strbuf *err)
 {
+	struct ref_dir *loose_refs = get_loose_refs(&ref_cache);
+	struct ref_dir *packed_refs = get_packed_refs(&ref_cache);
 	int ret = 0, i;
 	int n = transaction->nr;
 	struct ref_update **updates = transaction->updates;
@@ -4115,12 +4125,36 @@ int initial_ref_transaction_commit(struct ref_transaction *transaction,
 		goto cleanup;
 	}
 
+	/*
+	 * It's really undefined to call this function in an active
+	 * repository or when there are existing references: we are
+	 * only locking and changing packed-refs, so (1) any
+	 * simultaneous processes might try to change a reference at
+	 * the same time we do, and (2) any existing loose versions of
+	 * the references that we are setting would have precedence
+	 * over our values. But some remote helpers create the remote
+	 * "HEAD" and "master" branches before calling this function,
+	 * so here we really only check that none of the references
+	 * that we are creating already exists.
+	 */
+	if (for_each_rawref(ref_present, &affected_refnames))
+		die("BUG: initial ref transaction called with existing refs");
+
 	for (i = 0; i < n; i++) {
 		struct ref_update *update = updates[i];
 
 		if ((update->flags & REF_HAVE_OLD) &&
 		    !is_null_sha1(update->old_sha1))
 			die("BUG: initial ref transaction with old_sha1 set");
+		if (verify_refname_available(update->refname,
+					     &affected_refnames, NULL,
+					     loose_refs, err) ||
+		    verify_refname_available(update->refname,
+					     &affected_refnames, NULL,
+					     packed_refs, err)) {
+			ret = TRANSACTION_NAME_CONFLICT;
+			goto cleanup;
+		}
 	}
 
 	if (lock_packed_refs(0)) {