diff --git a/builtin/clone.c b/builtin/clone.c
index 8f86d99c51f099805c752ba460cf99e6a77891b0..fa535507587959a345bcfa65cc17b760b95039ab 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -1201,7 +1201,7 @@ int cmd_clone(int argc, const char **argv, const char *prefix)
 
 	update_remote_refs(refs, mapped_refs, remote_head_points_at,
 			   branch_top.buf, reflog_msg.buf, transport,
-			   !is_local && !filter_options.choice);
+			   !is_local);
 
 	update_head(our_head_points_at, remote_head, reflog_msg.buf);
 
diff --git a/t/t5616-partial-clone.sh b/t/t5616-partial-clone.sh
index 8a2bf86491f6b3cd23cad5b15f4e5df2c55589e4..44d8e80171a646bc6b4172a38763ca6355c94901 100755
--- a/t/t5616-partial-clone.sh
+++ b/t/t5616-partial-clone.sh
@@ -170,4 +170,52 @@ test_expect_success 'partial clone fetches blobs pointed to by refs even if norm
 	git -C dst fsck
 '
 
+. "$TEST_DIRECTORY"/lib-httpd.sh
+start_httpd
+
+# Converts bytes into a form suitable for inclusion in a sed command. For
+# example, "printf 'ab\r\n' | hex_unpack" results in '\x61\x62\x0d\x0a'.
+sed_escape () {
+	perl -e '$/ = undef; $input = <>; print unpack("H2" x length($input), $input)' |
+		sed 's/\(..\)/\\x\1/g'
+}
+
+test_expect_success 'upon cloning, check that all refs point to objects' '
+	SERVER="$HTTPD_DOCUMENT_ROOT_PATH/server" &&
+	rm -rf "$SERVER" repo &&
+	test_create_repo "$SERVER" &&
+	test_commit -C "$SERVER" foo &&
+	test_config -C "$SERVER" uploadpack.allowfilter 1 &&
+	test_config -C "$SERVER" uploadpack.allowanysha1inwant 1 &&
+
+	# Create a tag pointing to a blob.
+	BLOB=$(echo blob-contents | git -C "$SERVER" hash-object --stdin -w) &&
+	git -C "$SERVER" tag myblob "$BLOB" &&
+
+	# Craft a packfile not including that blob.
+	git -C "$SERVER" rev-parse HEAD |
+		git -C "$SERVER" pack-objects --stdout >incomplete.pack &&
+
+	# Replace the existing packfile with the crafted one. The protocol
+	# requires that the packfile be sent in sideband 1, hence the extra
+	# \x01 byte at the beginning.
+	printf "1,/packfile/!c %04x\\\\x01%s0000" \
+		"$(($(wc -c <incomplete.pack) + 5))" \
+		"$(sed_escape <incomplete.pack)" \
+		>"$HTTPD_ROOT_PATH/one-time-sed" &&
+
+	# Use protocol v2 because the sed command looks for the "packfile"
+	# section header.
+	test_config -C "$SERVER" protocol.version 2 &&
+	test_must_fail git -c protocol.version=2 clone \
+		--filter=blob:none $HTTPD_URL/one_time_sed/server repo 2>err &&
+
+	grep "did not send all necessary objects" err &&
+
+	# Ensure that the one-time-sed script was used.
+	! test -e "$HTTPD_ROOT_PATH/one-time-sed"
+'
+
+stop_httpd
+
 test_done