diff --git a/CHANGELOG.md b/CHANGELOG.md
index d55e2108..f50c565c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ Jupytext ChangeLog
 - Jupytext now support more characters in the cell metadata keys, to improve compatibility with `jupyterlab-slideshow` ([#1441](https://github.com/mwouts/jupytext/issues/1441)). Thanks to [Nicolas Thierry](https://github.com/nthiery) for this fix.
 - The function `find_jupytext_configuration_file` now works with relative directories ([#1440](https://github.com/mwouts/jupytext/issues/1440)). This fix was contributed by [Thierry Parmentelat](https://github.com/parmentelat).
 - We have fixed a parsing error for R Markdown files ([#1429](https://github.com/mwouts/jupytext/issues/1429))
+- Complex pairing formats are now supported on Windows ([#1028](https://github.com/mwouts/jupytext/issues/1028))
 
 **Changed**
 - We have updated the pre-commit hooks. The code is now formatted using `ruff format`, and updated for Python 3.9+ using https://github.com/asottile/pyupgrade ([#1423](https://github.com/mwouts/jupytext/issues/1423))
diff --git a/src/jupytext/paired_paths.py b/src/jupytext/paired_paths.py
index 0258215c..eaf08d4b 100644
--- a/src/jupytext/paired_paths.py
+++ b/src/jupytext/paired_paths.py
@@ -61,7 +61,15 @@ def join(left, right, sep):
 
 def separator(path):
     """Return the local path separator (always / in the contents manager)"""
-    if os.path.sep == "\\" and "\\" in path:
+    # On Windows, determine the appropriate separator
+    if os.path.sep == "\\":
+        # If path contains \, definitely use Windows separator
+        if "\\" in path:
+            return "\\"
+        # If path contains / but not \, it's probably a format string or contents manager path
+        if "/" in path:
+            return "/"
+        # Path has no separators (e.g., bare filename) - use OS separator
         return "\\"
     return "/"
 
diff --git a/tests/unit/test_paired_paths.py b/tests/unit/test_paired_paths.py
index 256df5b6..bf97f91e 100644
--- a/tests/unit/test_paired_paths.py
+++ b/tests/unit/test_paired_paths.py
@@ -99,6 +99,21 @@ def test_paired_paths_windows_no_subfolder():
         paired_paths(nb_file, "notebooks///ipynb", formats)
 
 
+def test_paired_paths_windows_relative():
+    """Test Windows pairing with relative paths and backslash as path separator, issue #1028"""
+    nb_file = "notebooks\\example.ipynb"
+    formats = "notebooks///ipynb,scripts///py:percent"
+    with mock.patch("os.path.sep", "\\"):
+        # Should not raise InconsistentPath
+        paths = paired_paths(nb_file, "notebooks///ipynb", formats)
+        # Verify the notebook path is in the paired paths
+        path_list = [p[0] for p in paths]
+        assert nb_file in path_list, f"Expected {nb_file} to be in paired paths {path_list}"
+        # Verify both paths use backslashes on Windows
+        assert paths[0][0] == "notebooks\\example.ipynb"
+        assert paths[1][0] == "scripts\\example.py"
+
+
 @pytest.mark.parametrize("os_path_sep", ["\\", "/"])
 def test_paired_path_dotdot_564(os_path_sep):
     main_path = os_path_sep.join(["examples", "tutorials", "colabs", "rigid_object_tutorial.ipynb"])