diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ad82bd8e5d..da5fb94d5e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -55,7 +55,7 @@ repos:
     hooks:
       - id: pylint
         name: pylint
-        entry: python3 script/run-in-env.py pylint
+        entry: python script/run-in-env.py pylint
         language: system
         types: [python]
         files: ^esphome/.+\.py$
@@ -68,5 +68,5 @@ repos:
         additional_dependencies: []
       - id: ci-custom
         name: ci-custom
-        entry: python3 script/run-in-env.py script/ci-custom.py
+        entry: python script/run-in-env.py script/ci-custom.py
         language: system
diff --git a/script/ci-custom.py b/script/ci-custom.py
index b257a3818b..8cd8fd7544 100755
--- a/script/ci-custom.py
+++ b/script/ci-custom.py
@@ -250,7 +250,7 @@ def lint_ext_check(fname):
     ]
 )
 def lint_executable_bit(fname: Path) -> str | None:
-    ex = EXECUTABLE_BIT[str(fname)]
+    ex = EXECUTABLE_BIT[fname.as_posix()]
     if ex != 100644:
         return (
             f"File has invalid executable bit {ex}. If running from a windows machine please "
diff --git a/script/run-in-env.py b/script/run-in-env.py
index 9283ba9940..996db60554 100755
--- a/script/run-in-env.py
+++ b/script/run-in-env.py
@@ -44,7 +44,14 @@ def find_and_activate_virtualenv():
 def run_command():
     # Execute the remaining arguments in the new environment
     if len(sys.argv) > 1:
-        result = subprocess.run(sys.argv[1:], check=False, close_fds=False)
+        args = sys.argv[1:]
+        # Windows CreateProcess doesn't follow shebangs, so prepend the
+        # current interpreter when the entry is a .py script. Using
+        # sys.executable also pins the nested call to the same Python that
+        # ran us — no ambiguous PATH lookup for "python".
+        if args[0].endswith(".py"):
+            args = [sys.executable, *args]
+        result = subprocess.run(args, check=False, close_fds=False)
         sys.exit(result.returncode)
     else:
         print(