diff --git a/scalar.c b/scalar.c
index 611831e33fcc19..9cedb21bbc6438 100644
--- a/scalar.c
+++ b/scalar.c
@@ -1028,7 +1028,6 @@ static int cmd_reconfigure(int argc, const char **argv)
 	};
 	struct string_list scalar_repos = STRING_LIST_INIT_DUP;
 	int i, res = 0;
-	struct repository r = { NULL };
 	struct strbuf commondir = STRBUF_INIT, gitdir = STRBUF_INIT;
 
 	argc = parse_options(argc, argv, NULL, options,
@@ -1048,6 +1047,7 @@ static int cmd_reconfigure(int argc, const char **argv)
 
 	for (i = 0; i < scalar_repos.nr; i++) {
 		int succeeded = 0;
+		struct repository *old_repo, r = { NULL };
 		const char *dir = scalar_repos.items[i].string;
 
 		strbuf_reset(&commondir);
@@ -1095,14 +1095,18 @@ static int cmd_reconfigure(int argc, const char **argv)
 
 		git_config_clear();
 
+		if (repo_init(&r, gitdir.buf, commondir.buf))
+			goto loop_end;
+
+		old_repo = the_repository;
 		the_repository = &r;
-		r.commondir = commondir.buf;
-		r.gitdir = gitdir.buf;
 
 		if (set_recommended_config(1) >= 0 &&
 		    toggle_maintenance(1) >= 0)
 			succeeded = 1;
 
+		the_repository = old_repo;
+
 loop_end:
 		if (!succeeded) {
 			res = -1;
diff --git a/t/t9210-scalar.sh b/t/t9210-scalar.sh
index ac3b8b3a02bfdf..dcb80340e9e851 100755
--- a/t/t9210-scalar.sh
+++ b/t/t9210-scalar.sh
@@ -190,6 +190,44 @@ test_expect_success 'scalar reconfigure' '
 	test_subcommand git maintenance start <reconfigure
 '
 
+test_expect_success 'scalar reconfigure --all with includeIf.onbranch' '
+	repos="two three four" &&
+	for num in $repos
+	do
+		git init $num/src &&
+		scalar register $num/src &&
+		git -C $num/src config includeif."onbranch:foo".path something &&
+		git -C $num/src config core.preloadIndex false || return 1
+	done &&
+
+	scalar reconfigure --all &&
+
+	for num in $repos
+	do
+		test true = "$(git -C $num/src config core.preloadIndex)" || return 1
+	done
+'
+
+ test_expect_success 'scalar reconfigure --all with detached HEADs' '
+	repos="two three four" &&
+	for num in $repos
+	do
+		rm -rf $num/src &&
+		git init $num/src &&
+		scalar register $num/src &&
+		git -C $num/src config core.preloadIndex false &&
+		test_commit -C $num/src initial &&
+		git -C $num/src switch --detach HEAD || return 1
+	done &&
+
+	scalar reconfigure --all &&
+
+	for num in $repos
+	do
+		test true = "$(git -C $num/src config core.preloadIndex)" || return 1
+	done
+'
+
 test_expect_success '`reconfigure -a` removes stale config entries' '
 	git init stale/src &&
 	scalar register stale &&