diff --git a/snakefmt/formatter.py b/snakefmt/formatter.py
index 43345bc..562bbd4 100644
--- a/snakefmt/formatter.py
+++ b/snakefmt/formatter.py
@@ -143,7 +143,8 @@ def run_black_format_str(
         inside_nested_statement = (
             self.syntax.code_indent is not None and self.syntax.code_indent > 0
         )
-        if inside_nested_statement and self.from_python:  # i.e. after snakecode
+        # this checks if we are inside snakecode, within a nested if-else statement
+        if inside_nested_statement and self.from_python and self.in_global_context:
             # indent any comments and the first line
             tmpstring = ""
             for i, line in enumerate(string.splitlines(keepends=True)):
diff --git a/tests/test_formatter.py b/tests/test_formatter.py
index 6fee652..ed335e2 100644
--- a/tests/test_formatter.py
+++ b/tests/test_formatter.py
@@ -523,6 +523,22 @@ def test_nested_if_statements_with_comments_and_snakecode_inside2(self):
         formatter = setup_formatter(snakecode)
         assert formatter.get_formatted() == snakecode
 
+    def test_nested_if_statements_with_comments_and_snakecode_inside3(self):
+        """https://github.com/snakemake/snakefmt/pull/136#issuecomment-1132845522"""
+        snakecode = (
+            "if True:\n\n"
+            f"{TAB * 1}rule with_run_directive:\n"
+            f"{TAB * 2}output:\n"
+            f'{TAB * 3}"test.txt",\n'
+            f"{TAB * 2}run:\n"
+            f"{TAB * 3}if True:\n"
+            f'{TAB * 4}print("this line is in the error")\n'
+            "\n\n"
+            f'{TAB * 1}print("the indenting on this line matters")\n'
+        )
+        formatter = setup_formatter(snakecode)
+        assert formatter.get_formatted() == snakecode
+
     def test_nested_if_statements_with_function_and_snakecode_inside(self):
         """https://github.com/snakemake/snakefmt/pull/136#issuecomment-1125130038"""
         snakecode = (