diff --git a/isort/core.py b/isort/core.py
index 472d914d..1f56f713 100644
--- a/isort/core.py
+++ b/isort/core.py
@@ -340,10 +340,12 @@ def process(
                         ):
                             cimport_statement = True
 
-                        if cimport_statement != cimports or (
+                        if cimport_statement != cimports:
+                            indent = new_indent
+                        if (
                             new_indent != indent
                             and import_section
-                            and (not did_contain_imports or len(new_indent) < len(indent))
+                            and (not did_contain_imports and len(new_indent) < len(indent))
                         ):
                             indent = new_indent
                             if import_section:
@@ -421,7 +423,7 @@ def process(
 
                     if indent:
                         import_section = "".join(
-                            line[len(indent) :] for line in import_section.splitlines(keepends=True)
+                            line[len(line) - len(line.lstrip()) :] for line in import_section.splitlines(keepends=True)
                         )
 
                     parsed_content = parse.file_contents(import_section, config=config)
diff --git a/tests/unit/test_isort.py b/tests/unit/test_isort.py
index c241e325..3a7d5525 100644
--- a/tests/unit/test_isort.py
+++ b/tests/unit/test_isort.py
@@ -5689,6 +5689,22 @@ def test_reexport_not_last_line() -> None:
     assert isort.code(test_input, config=Config(sort_reexports=True)) == expd_output
 
 
+def test_strip_leading_characters_with_odd_indentation() -> None:
+    """ Test to ensure that isort doesn't strip away leading character
+    with odd indentation
+    """
+    test_input = """
+#!/usr/bin/env python3
+
+if True:
+#this comment breaks
+    # this is another comment
+    import sys
+    """
+
+    assert isort.code(test_input) == test_input
+
+
 def test_reexport_multiline_import() -> None:
     test_input = """from m import (
     bar,