diff --git a/conda_smithy/feedstock_io.py b/conda_smithy/feedstock_io.py
index 7e4146cf1..54d18aba9 100644
--- a/conda_smithy/feedstock_io.py
+++ b/conda_smithy/feedstock_io.py
@@ -87,7 +87,10 @@ def remove_file_or_dir(filename):
 
     repo = get_repo(filename)
     if repo:
-        repo.index.remove_all(["filename/**"])
+        index_path = (
+            Path(filename).resolve().relative_to(repo.workdir).as_posix()
+        )
+        repo.index.remove_all([f"{index_path}/**"])
         repo.index.write()
     shutil.rmtree(filename)
 
diff --git a/news/fix-feedstock_io-dir-remove.rst b/news/fix-feedstock_io-dir-remove.rst
new file mode 100644
index 000000000..8ee248b2a
--- /dev/null
+++ b/news/fix-feedstock_io-dir-remove.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed removing directories recursively from git index. (#2199)
+
+**Security:**
+
+* <news item>
diff --git a/tests/test_feedstock_io.py b/tests/test_feedstock_io.py
index b8c188cac..eb6ee4b84 100644
--- a/tests/test_feedstock_io.py
+++ b/tests/test_feedstock_io.py
@@ -178,6 +178,33 @@ def test_remove_file(self):
                     repo.index.read()
                     self.assertRaises(KeyError, lambda: repo.index[basename])
 
+    def test_remove_dir(self):
+        for tmp_dir, repo, pathfunc in parameterize():
+            dirname = os.path.join(tmp_dir, "dir")
+            os.makedirs(f"{dirname}/a")
+            os.makedirs(f"{dirname}/b")
+            for basename in ["dir/a/foo.txt", "dir/b/bar.txt", "dir/baz.txt"]:
+                filename = os.path.join(tmp_dir, basename)
+
+                with open(filename, "w", encoding="utf-8", newline="\n") as fh:
+                    fh.write("")
+                if repo is not None:
+                    repo.index.add(basename)
+                    repo.index.write()
+
+                self.assertTrue(os.path.exists(filename))
+                if repo is not None:
+                    self.assertIsNotNone(repo.index[basename])
+
+            fio.remove_file_or_dir(pathfunc(dirname))
+
+            for basename in ["dir/a/foo.txt", "dir/b/bar.txt", "dir/baz.txt"]:
+                self.assertFalse(os.path.exists(filename))
+                if repo is not None:
+                    repo.index.read()
+                    self.assertRaises(KeyError, lambda: repo.index[basename])
+            self.assertFalse(os.path.exists(dirname))
+
     def test_copy_file(self):
         for tmp_dir, repo, pathfunc in parameterize():
             basename1 = "test1.txt"