diff --git a/scalar.c b/scalar.c
index 03f9e480dd..6c52243cdf 100644
--- a/scalar.c
+++ b/scalar.c
@@ -596,6 +596,24 @@ static int get_scalar_repos(const char *key, const char *value, void *data)
 	return 0;
 }
 
+static int remove_deleted_enlistment(struct strbuf *path)
+{
+	int res = 0;
+	strbuf_realpath_forgiving(path, path->buf, 1);
+
+	if (run_git("config", "--global",
+		    "--unset", "--fixed-value",
+		    "scalar.repo", path->buf, NULL) < 0)
+		res = -1;
+
+	if (run_git("config", "--global",
+		    "--unset", "--fixed-value",
+		    "maintenance.repo", path->buf, NULL) < 0)
+		res = -1;
+
+	return res;
+}
+
 static int cmd_reconfigure(int argc, const char **argv)
 {
 	int all = 0;
@@ -635,8 +653,22 @@ static int cmd_reconfigure(int argc, const char **argv)
 		strbuf_reset(&gitdir);
 
 		if (chdir(dir) < 0) {
-			warning_errno(_("could not switch to '%s'"), dir);
-			res = -1;
+			struct strbuf buf = STRBUF_INIT;
+
+			if (errno != ENOENT) {
+				warning_errno(_("could not switch to '%s'"), dir);
+				res = -1;
+				continue;
+			}
+
+			strbuf_addstr(&buf, dir);
+			if (remove_deleted_enlistment(&buf))
+				res = error(_("could not remove stale "
+					      "scalar.repo '%s'"), dir);
+			else
+				warning(_("removing stale scalar.repo '%s'"),
+					dir);
+			strbuf_release(&buf);
 		} else if (discover_git_directory(&commondir, &gitdir) < 0) {
 			warning_errno(_("git repository gone in '%s'"), dir);
 			res = -1;
@@ -722,24 +754,6 @@ static int cmd_run(int argc, const char **argv)
 	return 0;
 }
 
-static int remove_deleted_enlistment(struct strbuf *path)
-{
-	int res = 0;
-	strbuf_realpath_forgiving(path, path->buf, 1);
-
-	if (run_git("config", "--global",
-		    "--unset", "--fixed-value",
-		    "scalar.repo", path->buf, NULL) < 0)
-		res = -1;
-
-	if (run_git("config", "--global",
-		    "--unset", "--fixed-value",
-		    "maintenance.repo", path->buf, NULL) < 0)
-		res = -1;
-
-	return res;
-}
-
 static int cmd_unregister(int argc, const char **argv)
 {
 	struct option options[] = {
diff --git a/t/t9210-scalar.sh b/t/t9210-scalar.sh
index be51a8bb7a..25f500cf68 100755
--- a/t/t9210-scalar.sh
+++ b/t/t9210-scalar.sh
@@ -166,6 +166,20 @@ test_expect_success 'scalar reconfigure' '
 	test true = "$(git -C one/src config core.preloadIndex)"
 '
 
+test_expect_success '`reconfigure -a` removes stale config entries' '
+	git init stale/src &&
+	scalar register stale &&
+	scalar list >scalar.repos &&
+	grep stale scalar.repos &&
+
+	grep -v stale scalar.repos >expect &&
+
+	rm -rf stale &&
+	scalar reconfigure -a &&
+	scalar list >scalar.repos &&
+	test_cmp expect scalar.repos
+'
+
 test_expect_success 'scalar delete without enlistment shows a usage' '
 	test_expect_code 129 scalar delete
 '