diff --git a/check/main.c b/check/main.c
index db055ae19..880827e11 100644
--- a/check/main.c
+++ b/check/main.c
@@ -87,6 +87,7 @@ bool is_free_space_tree = false;
 bool init_extent_tree = false;
 bool check_data_csum = false;
 static bool found_free_ino_cache = false;
+static bool found_unknown_key = false;
 struct cache_tree *roots_info_cache = NULL;
 
 enum btrfs_check_mode {
@@ -1895,6 +1896,10 @@ static int process_one_leaf(struct btrfs_root *root, struct extent_buffer *eb,
 			ret = process_xattr_item(eb, i, &key, active_node);
 			break;
 		default:
+			error("Unknown key (%llu %u %llu) found in leaf %llu",
+			      key.objectid, key.type, key.offset,
+			      eb->start);
+			found_unknown_key = true;
 			break;
 		};
 	}
@@ -2346,6 +2351,42 @@ static int create_inode_item(struct btrfs_root *root,
 	return 0;
 }
 
+static int create_inode_ref(struct btrfs_root *root,
+			    struct inode_record *i_rec,
+			    struct inode_backref *backref)
+{
+	struct btrfs_trans_handle *trans;
+	int ret;
+
+	trans = btrfs_start_transaction(root, 1);
+	if (IS_ERR(trans)) {
+		ret = PTR_ERR(trans);
+		errno = -ret;
+		error_msg(ERROR_MSG_START_TRANS, "%m");
+		return ret;
+	}
+
+	ret = btrfs_insert_inode_ref(trans, root, backref->name, backref->namelen,
+				     i_rec->ino, backref->dir, backref->index);
+	if (ret < 0) {
+		btrfs_commit_transaction(trans, root);
+		return ret;
+	}
+	ret = btrfs_commit_transaction(trans, root);
+	if (ret < 0) {
+		ret = PTR_ERR(trans);
+		errno = -ret;
+		error_msg(ERROR_MSG_COMMIT_TRANS, "%m");
+		return ret;
+	}
+	backref->found_inode_ref = 1;
+	backref->errors &= ~REF_ERR_NO_INODE_REF;
+	printf("Added INODE_REF for root %lld ino %llu parent %llu index %llu name %.*s\n",
+		btrfs_root_id(root), i_rec->ino, backref->dir, backref->index,
+		backref->namelen, backref->name);
+	return 0;
+}
+
 static int repair_inode_backrefs(struct btrfs_root *root,
 				 struct inode_record *rec,
 				 struct cache_tree *inode_cache,
@@ -2370,6 +2411,21 @@ static int repair_inode_backrefs(struct btrfs_root *root,
 		if (rec->ino == root_dirid && backref->index == 0)
 			continue;
 
+		/*
+		 * Have DIR_INDEX, DIR_ITEM and INODE_ITEM, and even nlinks
+		 * matches with only missing INODE_REF.
+		 */
+		if (!backref->found_inode_ref && backref->found_dir_item &&
+		    backref->found_dir_index && rec->found_inode_item &&
+		    rec->found_link == rec->nlink) {
+			ret = create_inode_ref(root, rec, backref);
+			if (ret)
+				break;
+			repaired++;
+			list_del(&backref->list);
+			free(backref);
+			continue;
+		}
 		if (delete &&
 		    ((backref->found_dir_index && !backref->found_inode_ref) ||
 		     (backref->found_dir_index && backref->found_inode_ref &&
@@ -4027,6 +4083,8 @@ static int check_fs_roots(struct cache_tree *root_cache)
 		free_extent_cache_tree(&wc.shared);
 	if (!cache_tree_empty(&wc.shared))
 		fprintf(stderr, "warning line %d\n", __LINE__);
+	if (!err && found_unknown_key)
+		err = 1;
 
 	return err;
 }
diff --git a/check/mode-lowmem.c b/check/mode-lowmem.c
index ea4d40178..dcec6cc06 100644
--- a/check/mode-lowmem.c
+++ b/check/mode-lowmem.c
@@ -1015,6 +1015,17 @@ static int repair_ternary_lowmem(struct btrfs_root *root, u64 dir_ino, u64 ino,
 	int stage = 0;
 	int ret = 0;
 
+	/*
+	 * We miss an INODE_REF, and we're checking DIR_ITEM and hasn't yet
+	 * find the DIR_INDEX, thus there is no reliable index.
+	 * Try to locate one, this can be slow as we need to locate the DIR_INDEX
+	 * item from the directory.
+	 */
+	if (index == (u64)-1 && (err & INODE_REF_MISSING)) {
+		ret = find_dir_index(root, dir_ino, ino, &index, name, name_len, filetype);
+		if (ret < 0)
+			err |= DIR_INDEX_MISSING;
+	}
 	/*
 	 * stage shall be one of following valild values:
 	 *	0: Fine, nothing to do.
@@ -2808,8 +2819,9 @@ static int check_inode_item(struct btrfs_root *root, struct btrfs_path *path)
 		case BTRFS_XATTR_ITEM_KEY:
 			break;
 		default:
-			error("ITEM[%llu %u %llu] UNKNOWN TYPE",
-			      key.objectid, key.type, key.offset);
+			error("ITEM[%llu %u %llu] UNKNOWN TYPE in leaf %llu",
+			      key.objectid, key.type, key.offset, node->start);
+			err |= UNKNOWN_KEY;
 		}
 	}
 
diff --git a/check/mode-lowmem.h b/check/mode-lowmem.h
index cd0355465..ec199b4c8 100644
--- a/check/mode-lowmem.h
+++ b/check/mode-lowmem.h
@@ -48,6 +48,7 @@
 #define INVALID_GENERATION	(1U << 26)	/* Generation is too new */
 #define SUPER_BYTES_USED_ERROR	(1U << 27)	/* Super bytes_used is invalid */
 #define DUP_FILENAME_ERROR	(1U << 28)	/* DIR_ITEM contains duplicate names */
+#define UNKNOWN_KEY		(1U << 29)	/* Found unknown key type in fs trees */
 
 /*
  * Error bit for low memory mode check.
diff --git a/tests/fsck-tests/069-unknown-fs-tree-key/test.sh b/tests/fsck-tests/069-unknown-fs-tree-key/test.sh
new file mode 100755
index 000000000..ea4f04e28
--- /dev/null
+++ b/tests/fsck-tests/069-unknown-fs-tree-key/test.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#
+# Verify that check can report unknown key types in subvolume trees
+
+source "$TEST_TOP/common" || exit
+
+check_prereq btrfs
+
+check_image() {
+	run_mustfail "unknown keys in subvolume trees not reported as error" \
+		"$TOP/btrfs" check "$1"
+}
+
+check_all_images
diff --git a/tests/fsck-tests/069-unknown-fs-tree-key/unknown_key_empty.img.xz b/tests/fsck-tests/069-unknown-fs-tree-key/unknown_key_empty.img.xz
new file mode 100644
index 000000000..300a7cc92
Binary files /dev/null and b/tests/fsck-tests/069-unknown-fs-tree-key/unknown_key_empty.img.xz differ
diff --git a/tests/fsck-tests/070-missing-inode-ref/.lowmem_repairable b/tests/fsck-tests/070-missing-inode-ref/.lowmem_repairable
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/fsck-tests/070-missing-inode-ref/default.img.xz b/tests/fsck-tests/070-missing-inode-ref/default.img.xz
new file mode 100644
index 000000000..15d95eed3
Binary files /dev/null and b/tests/fsck-tests/070-missing-inode-ref/default.img.xz differ