diff --git a/commit.c b/commit.c
index 98b2e55665..ffcc4a97cd 100644
--- a/commit.c
+++ b/commit.c
@@ -249,6 +249,16 @@ int for_each_commit_graft(each_commit_graft_fn fn, void *cb_data)
 	return ret;
 }
 
+void reset_commit_grafts(struct repository *r)
+{
+	int i;
+
+	for (i = 0; i < r->parsed_objects->grafts_nr; i++)
+		free(r->parsed_objects->grafts[i]);
+	r->parsed_objects->grafts_nr = 0;
+	r->parsed_objects->commit_graft_prepared = 0;
+}
+
 struct commit_buffer {
 	void *buffer;
 	unsigned long size;
diff --git a/commit.h b/commit.h
index 3b174135bc..21e4d25ce7 100644
--- a/commit.h
+++ b/commit.h
@@ -249,6 +249,7 @@ int commit_graft_pos(struct repository *r, const struct object_id *oid);
 int register_commit_graft(struct repository *r, struct commit_graft *, int);
 void prepare_commit_graft(struct repository *r);
 struct commit_graft *lookup_commit_graft(struct repository *r, const struct object_id *oid);
+void reset_commit_grafts(struct repository *r);
 
 struct commit *get_fork_point(const char *refname, struct commit *commit);
 
diff --git a/shallow.c b/shallow.c
index 71e5876f37..e158be58b0 100644
--- a/shallow.c
+++ b/shallow.c
@@ -90,6 +90,7 @@ static void reset_repository_shallow(struct repository *r)
 {
 	r->parsed_objects->is_shallow = -1;
 	stat_validity_clear(r->parsed_objects->shallow_stat);
+	reset_commit_grafts(r);
 }
 
 int commit_shallow_file(struct repository *r, struct shallow_lock *lk)
diff --git a/submodule.c b/submodule.c
index 5ace18a7d9..7a0515913c 100644
--- a/submodule.c
+++ b/submodule.c
@@ -22,6 +22,7 @@
 #include "parse-options.h"
 #include "object-store.h"
 #include "commit-reach.h"
+#include "shallow.h"
 
 static int config_update_recurse_submodules = RECURSE_SUBMODULES_OFF;
 static int initialized_fetch_ref_tips;
diff --git a/t/t5537-fetch-shallow.sh b/t/t5537-fetch-shallow.sh
index 11d5ea54a9..92948de7a0 100755
--- a/t/t5537-fetch-shallow.sh
+++ b/t/t5537-fetch-shallow.sh
@@ -161,6 +161,15 @@ test_expect_success 'fetch --update-shallow' '
 	)
 '
 
+test_expect_success 'fetch --update-shallow into a repo with submodules' '
+	git init a-submodule &&
+	test_commit -C a-submodule foo &&
+	git init repo-with-sub &&
+	git -C repo-with-sub submodule add ../a-submodule a-submodule &&
+	git -C repo-with-sub commit -m "added submodule" &&
+	git -C repo-with-sub fetch --update-shallow ../shallow/.git refs/heads/*:refs/remotes/shallow/*
+'
+
 test_expect_success 'fetch --update-shallow (with fetch.writeCommitGraph)' '
 	(
 	cd shallow &&