diff --git a/src/flb_fstore.c b/src/flb_fstore.c
index e02dbcd18ea..84b46fc1df2 100644
--- a/src/flb_fstore.c
+++ b/src/flb_fstore.c
@@ -215,12 +215,33 @@ struct flb_fstore_file *flb_fstore_file_get(struct flb_fstore *fs,
  * Set a file to inactive mode. Inactive means just to remove the reference
  * from the list.
  */
+static int chunk_is_linked_to_stream(struct flb_fstore_file *fsf)
+{
+    struct mk_list *head;
+    struct cio_chunk *chunk;
+
+    if (fsf == NULL || fsf->chunk == NULL || fsf->stream == NULL) {
+        return FLB_FALSE;
+    }
+
+    mk_list_foreach(head, &fsf->stream->chunks) {
+        chunk = mk_list_entry(head, struct cio_chunk, _head);
+
+        if (chunk == fsf->chunk) {
+            return FLB_TRUE;
+        }
+    }
+
+    return FLB_FALSE;
+}
+
 int flb_fstore_file_inactive(struct flb_fstore *fs,
                              struct flb_fstore_file *fsf)
 {
     /* close the Chunk I/O reference, but don't delete the real file */
-    if (fsf->chunk) {
+    if (chunk_is_linked_to_stream(fsf) == FLB_TRUE) {
         cio_chunk_close(fsf->chunk, CIO_FALSE);
+        fsf->chunk = NULL;
     }
 
     /* release */
@@ -239,7 +260,10 @@ int flb_fstore_file_delete(struct flb_fstore *fs,
                            struct flb_fstore_file *fsf)
 {
     /* close the Chunk I/O reference, but don't delete it the real file */
-    cio_chunk_close(fsf->chunk, CIO_TRUE);
+    if (chunk_is_linked_to_stream(fsf) == FLB_TRUE) {
+        cio_chunk_close(fsf->chunk, CIO_TRUE);
+        fsf->chunk = NULL;
+    }
 
     /* release */
     mk_list_del(&fsf->_head);
@@ -415,6 +439,7 @@ static int map_chunks(struct flb_fstore *ctx, struct flb_fstore_stream *fs_strea
             return -1;
         }
 
+        fsf->stream = stream;
         fsf->chunk = chunk;
 
         /* load metadata */
diff --git a/tests/internal/fstore.c b/tests/internal/fstore.c
index 1f4de61b567..8979378b400 100644
--- a/tests/internal/fstore.c
+++ b/tests/internal/fstore.c
@@ -30,6 +30,7 @@
 
 #include <sys/types.h>
 #include <sys/stat.h>
+#include <errno.h>
 
 #ifdef FLB_SYSTEM_WINDOWS
 /* Not yet implemented! */
@@ -78,7 +79,57 @@ void cb_all()
     flb_fstore_destroy(fs);
 }
 
+void cb_delete_after_external_close()
+{
+    int ret;
+    struct stat st_data;
+    struct flb_fstore *fs;
+    struct flb_fstore_stream *st;
+    struct flb_fstore_file *fsf;
+    struct cio_chunk *chunk;
+
+    cio_utils_recursive_delete(FSF_STORE_PATH);
+
+    fs = flb_fstore_create(FSF_STORE_PATH, FLB_FSTORE_FS);
+    TEST_CHECK(fs != NULL);
+    if (!fs) {
+        return;
+    }
+
+    st = flb_fstore_stream_create(fs, "abc");
+    TEST_CHECK(st != NULL);
+    if (!st) {
+        flb_fstore_destroy(fs);
+        return;
+    }
+
+    fsf = flb_fstore_file_create(fs, st, "example.txt", 100);
+    TEST_CHECK(fsf != NULL);
+    if (!fsf) {
+        flb_fstore_destroy(fs);
+        return;
+    }
+
+    chunk = fsf->chunk;
+    TEST_CHECK(chunk != NULL);
+    if (!chunk) {
+        flb_fstore_destroy(fs);
+        return;
+    }
+
+    cio_chunk_close(chunk, CIO_TRUE);
+
+    ret = stat(FSF_STORE_PATH "/abc/example.txt", &st_data);
+    TEST_CHECK(ret == -1 && errno == ENOENT);
+
+    ret = flb_fstore_file_delete(fs, fsf);
+    TEST_CHECK(ret == 0);
+
+    flb_fstore_destroy(fs);
+}
+
 TEST_LIST = {
     { "all" , cb_all},
+    { "delete_after_external_close", cb_delete_after_external_close},
     { NULL }
 };