diff --git a/builtin/prune.c b/builtin/prune.c
index 41230f8215..1ec9ddd751 100644
--- a/builtin/prune.c
+++ b/builtin/prune.c
@@ -161,7 +161,7 @@ int cmd_prune(int argc, const char **argv, const char *prefix)
 	free(s);
 
 	if (is_repository_shallow(the_repository))
-		prune_shallow(show_only);
+		prune_shallow(show_only ? PRUNE_SHOW_ONLY : 0);
 
 	return 0;
 }
diff --git a/builtin/repack.c b/builtin/repack.c
index 0223f2880c..82c19b7555 100644
--- a/builtin/repack.c
+++ b/builtin/repack.c
@@ -550,6 +550,12 @@ int cmd_repack(int argc, const char **argv, const char *prefix)
 		if (!po_args.quiet && isatty(2))
 			opts |= PRUNE_PACKED_VERBOSE;
 		prune_packed_objects(opts);
+
+		if (!keep_unreachable &&
+		    (!(pack_everything & LOOSEN_UNREACHABLE) ||
+		     unpack_unreachable) &&
+		    is_repository_shallow(the_repository))
+			prune_shallow(PRUNE_QUICK);
 	}
 
 	if (!no_update_server_info)
diff --git a/commit.h b/commit.h
index 6c4428c593..8f15cfd43b 100644
--- a/commit.h
+++ b/commit.h
@@ -251,7 +251,9 @@ extern void assign_shallow_commits_to_refs(struct shallow_info *info,
 					   uint32_t **used,
 					   int *ref_status);
 extern int delayed_reachability_test(struct shallow_info *si, int c);
-extern void prune_shallow(int show_only);
+#define PRUNE_SHOW_ONLY 1
+#define PRUNE_QUICK 2
+extern void prune_shallow(unsigned options);
 extern struct trace_key trace_shallow;
 
 extern int interactive_add(int argc, const char **argv, const char *prefix, int patch);
diff --git a/shallow.c b/shallow.c
index 732e18d54f..02fdbfc554 100644
--- a/shallow.c
+++ b/shallow.c
@@ -247,6 +247,7 @@ static void check_shallow_file_for_update(struct repository *r)
 
 #define SEEN_ONLY 1
 #define VERBOSE   2
+#define QUICK 4
 
 struct write_shallow_data {
 	struct strbuf *out;
@@ -261,7 +262,10 @@ static int write_one_shallow(const struct commit_graft *graft, void *cb_data)
 	const char *hex = oid_to_hex(&graft->oid);
 	if (graft->nr_parent != -1)
 		return 0;
-	if (data->flags & SEEN_ONLY) {
+	if (data->flags & QUICK) {
+		if (!has_object_file(&graft->oid))
+			return 0;
+	} else if (data->flags & SEEN_ONLY) {
 		struct commit *c = lookup_commit(the_repository, &graft->oid);
 		if (!c || !(c->object.flags & SEEN)) {
 			if (data->flags & VERBOSE)
@@ -371,16 +375,23 @@ void advertise_shallow_grafts(int fd)
 
 /*
  * mark_reachable_objects() should have been run prior to this and all
- * reachable commits marked as "SEEN".
+ * reachable commits marked as "SEEN", except when quick_prune is non-zero,
+ * in which case lines are excised from the shallow file if they refer to
+ * commits that do not exist (any longer).
  */
-void prune_shallow(int show_only)
+void prune_shallow(unsigned options)
 {
 	struct lock_file shallow_lock = LOCK_INIT;
 	struct strbuf sb = STRBUF_INIT;
+	unsigned flags = SEEN_ONLY;
 	int fd;
 
-	if (show_only) {
-		write_shallow_commits_1(&sb, 0, NULL, SEEN_ONLY | VERBOSE);
+	if (options & PRUNE_QUICK)
+		flags |= QUICK;
+
+	if (options & PRUNE_SHOW_ONLY) {
+		flags |= VERBOSE;
+		write_shallow_commits_1(&sb, 0, NULL, flags);
 		strbuf_release(&sb);
 		return;
 	}
@@ -388,7 +399,7 @@ void prune_shallow(int show_only)
 				       git_path_shallow(the_repository),
 				       LOCK_DIE_ON_ERROR);
 	check_shallow_file_for_update(the_repository);
-	if (write_shallow_commits_1(&sb, 0, NULL, SEEN_ONLY)) {
+	if (write_shallow_commits_1(&sb, 0, NULL, flags)) {
 		if (write_in_full(fd, sb.buf, sb.len) < 0)
 			die_errno("failed to write to %s",
 				  get_lock_file_path(&shallow_lock));
diff --git a/t/t5537-fetch-shallow.sh b/t/t5537-fetch-shallow.sh
index 7045685e2d..6faf17e17a 100755
--- a/t/t5537-fetch-shallow.sh
+++ b/t/t5537-fetch-shallow.sh
@@ -186,6 +186,33 @@ EOF
 	test_cmp expect actual
 '
 
+test_expect_success '.git/shallow is edited by repack' '
+	git init shallow-server &&
+	test_commit -C shallow-server A &&
+	test_commit -C shallow-server B &&
+	git -C shallow-server checkout -b branch &&
+	test_commit -C shallow-server C &&
+	test_commit -C shallow-server E &&
+	test_commit -C shallow-server D &&
+	d="$(git -C shallow-server rev-parse --verify D^0)" &&
+	git -C shallow-server checkout master &&
+
+	git clone --depth=1 --no-tags --no-single-branch \
+		"file://$PWD/shallow-server" shallow-client &&
+
+	: now remove the branch and fetch with prune &&
+	git -C shallow-server branch -D branch &&
+	git -C shallow-client fetch --prune --depth=1 \
+		origin "+refs/heads/*:refs/remotes/origin/*" &&
+	git -C shallow-client repack -adfl &&
+	test_must_fail git -C shallow-client rev-parse --verify $d^0 &&
+	! grep $d shallow-client/.git/shallow &&
+
+	git -C shallow-server branch branch-orig $d &&
+	git -C shallow-client fetch --prune --depth=2 \
+		origin "+refs/heads/*:refs/remotes/origin/*"
+'
+
 . "$TEST_DIRECTORY"/lib-httpd.sh
 start_httpd