diff --git a/src/comments.py b/src/comments.py
index 8031775..6fc7355 100644
--- a/src/comments.py
+++ b/src/comments.py
@@ -176,19 +176,30 @@ def parse_update_instructions(comment_body):
     # treated as global to avoid misclassifying example filenames as per-file
     # instructions.
     global_lines = []
-    in_code_fence = False
+    fence_char = None
     for line in lines:
         stripped = line.strip()
         if not stripped:
             global_lines.append("")
             continue
-        # Toggle code fence state on lines starting with triple backticks
-        # or triple tildes (handles language specifiers like ```python)
-        if stripped.startswith("```") or stripped.startswith("~~~"):
-            in_code_fence = not in_code_fence
+        # Track code fence state with delimiter awareness: a fence opened
+        # with backticks can only be closed by backticks, and likewise for
+        # tildes (CommonMark spec §4.5).
+        if stripped.startswith("```"):
+            if fence_char is None:
+                fence_char = "`"
+            elif fence_char == "`":
+                fence_char = None
             global_lines.append(stripped)
             continue
-        if in_code_fence:
+        if stripped.startswith("~~~"):
+            if fence_char is None:
+                fence_char = "~"
+            elif fence_char == "~":
+                fence_char = None
+            global_lines.append(stripped)
+            continue
+        if fence_char is not None:
             global_lines.append(stripped)
             continue
         file_match = file_pattern.match(stripped)
diff --git a/tests/test_comment_parsing.py b/tests/test_comment_parsing.py
index 07d43a3..77ab646 100644
--- a/tests/test_comment_parsing.py
+++ b/tests/test_comment_parsing.py
@@ -191,6 +191,33 @@ def test_unclosed_code_fence_treats_rest_as_global(self):
         assert "config.md: another example" in global_inst
         assert file_inst == {}
 
+    def test_cross_delimiter_fence_not_closed(self):
+        """A backtick-opened fence should not be closed by tilde delimiters."""
+        comment = "[update-docs] Update the docs:\n```\n~~~\nfile.rst: add a new section\n```\n"
+        global_inst, file_inst = parse_update_instructions(comment)
+        # ~~~ should not close the backtick fence, so file.rst line
+        # remains inside the fence and is not a per-file instruction
+        assert "file.rst" not in file_inst
+        assert "file.rst: add a new section" in global_inst
+
+    def test_cross_delimiter_tilde_opened_backtick_no_close(self):
+        """A tilde-opened fence should not be closed by backtick delimiters."""
+        comment = (
+            "[update-docs] see this:\n"
+            "~~~\n"
+            "```\n"
+            "config.rst: update settings\n"
+            "~~~\n"
+            "health.md: fix intro"
+        )
+        global_inst, file_inst = parse_update_instructions(comment)
+        # ``` should not close the tilde fence, so config.rst stays global
+        assert "config.rst" not in file_inst
+        assert "config.rst: update settings" in global_inst
+        # health.md is after the tilde fence closes, so it is per-file
+        assert "health.md" in file_inst
+        assert file_inst["health.md"] == "fix intro"
+
 
 # ── _resolve_file_instructions ───────────────────────────────────────────────