diff --git a/builtin/add.c b/builtin/add.c
index 03ee5a3a7a2e35..620430cabf6f3d 100644
--- a/builtin/add.c
+++ b/builtin/add.c
@@ -5,6 +5,7 @@
  */
 #define USE_THE_INDEX_VARIABLE
 #include "builtin.h"
+#include "environment.h"
 #include "advice.h"
 #include "config.h"
 #include "lockfile.h"
@@ -48,6 +49,7 @@ static int chmod_pathspec(struct pathspec *pathspec, char flip, int show_only)
 		int err;
 
 		if (!include_sparse &&
+		    !core_virtualfilesystem &&
 		    (ce_skip_worktree(ce) ||
 		     !path_in_sparse_checkout(ce->name, &the_index)))
 			continue;
@@ -128,8 +130,9 @@ static int refresh(int verbose, const struct pathspec *pathspec)
 		if (!seen[i]) {
 			const char *path = pathspec->items[i].original;
 
-			if (matches_skip_worktree(pathspec, i, &skip_worktree_seen) ||
-			    !path_in_sparse_checkout(path, &the_index)) {
+			if (!core_virtualfilesystem &&
+			    (matches_skip_worktree(pathspec, i, &skip_worktree_seen) ||
+			     !path_in_sparse_checkout(path, &the_index))) {
 				string_list_append(&only_match_skip_worktree,
 						   pathspec->items[i].original);
 			} else {
@@ -139,7 +142,11 @@ static int refresh(int verbose, const struct pathspec *pathspec)
 		}
 	}
 
-	if (only_match_skip_worktree.nr) {
+	/*
+	 * When using a virtual filesystem, we might re-add a path
+	 * that is currently virtual and we want that to succeed.
+	 */
+	if (!core_virtualfilesystem && only_match_skip_worktree.nr) {
 		advise_on_updating_sparse_paths(&only_match_skip_worktree);
 		ret = 1;
 	}
@@ -517,7 +524,11 @@ int cmd_add(int argc, const char **argv, const char *prefix)
 			if (seen[i])
 				continue;
 
-			if (!include_sparse &&
+			/*
+			 * When using a virtual filesystem, we might re-add a path
+			 * that is currently virtual and we want that to succeed.
+			 */
+			if (!include_sparse && !core_virtualfilesystem &&
 			    matches_skip_worktree(&pathspec, i, &skip_worktree_seen)) {
 				string_list_append(&only_match_skip_worktree,
 						   pathspec.items[i].original);
@@ -541,7 +552,6 @@ int cmd_add(int argc, const char **argv, const char *prefix)
 			}
 		}
 
-
 		if (only_match_skip_worktree.nr) {
 			advise_on_updating_sparse_paths(&only_match_skip_worktree);
 			exit_status = 1;
diff --git a/builtin/rm.c b/builtin/rm.c
index dff819ae5098ff..82501a3df8ada1 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -5,6 +5,7 @@
  */
 #define USE_THE_INDEX_VARIABLE
 #include "builtin.h"
+#include "environment.h"
 #include "advice.h"
 #include "config.h"
 #include "lockfile.h"
@@ -312,7 +313,7 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	for (i = 0; i < the_index.cache_nr; i++) {
 		const struct cache_entry *ce = the_index.cache[i];
 
-		if (!include_sparse &&
+		if (!include_sparse && !core_virtualfilesystem &&
 		    (ce_skip_worktree(ce) ||
 		     !path_in_sparse_checkout(ce->name, &the_index)))
 			continue;
@@ -349,7 +350,11 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 				    *original ? original : ".");
 		}
 
-		if (only_match_skip_worktree.nr) {
+		/*
+		 * When using a virtual filesystem, we might re-add a path
+		 * that is currently virtual and we want that to succeed.
+		 */
+		if (!core_virtualfilesystem && only_match_skip_worktree.nr) {
 			advise_on_updating_sparse_paths(&only_match_skip_worktree);
 			ret = 1;
 		}
diff --git a/read-cache.c b/read-cache.c
index a08daf87dcd1ae..ea7e08f350b35e 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -3943,7 +3943,7 @@ static void update_callback(struct diff_queue_struct *q,
 		struct diff_filepair *p = q->queue[i];
 		const char *path = p->one->path;
 
-		if (!data->include_sparse &&
+		if (!data->include_sparse && !core_virtualfilesystem &&
 		    !path_in_sparse_checkout(path, data->index))
 			continue;