diff --git a/spyder/plugins/editor/widgets/codeeditor.py b/spyder/plugins/editor/widgets/codeeditor.py
index 966297b6ab6..11866f88300 100644
--- a/spyder/plugins/editor/widgets/codeeditor.py
+++ b/spyder/plugins/editor/widgets/codeeditor.py
@@ -1747,7 +1747,11 @@ def _apply_document_edits(self, edits):
         if edits is None:
             return
 
-        text = self.get_text_with_eol()
+        # We need to use here toPlainText and not get_text_with_eol to
+        # to not mess up the code when applying formatting.
+        # See spyder-ide/spyder#16180
+        text = self.toPlainText()
+
         text_tokens = list(text)
         merged_text = None
         for edit in edits: