diff --git a/asv_bench/benchmarks/package.py b/asv_bench/benchmarks/package.py
index 34fe4929a752b..257c82cba8878 100644
--- a/asv_bench/benchmarks/package.py
+++ b/asv_bench/benchmarks/package.py
@@ -11,7 +11,7 @@ def time_import(self):
         #  measurement of the import time we actually care about,
         #  without the subprocess or interpreter overhead
         cmd = [sys.executable, "-X", "importtime", "-c", "import pandas as pd"]
-        p = subprocess.run(cmd, stderr=subprocess.PIPE)
+        p = subprocess.run(cmd, stderr=subprocess.PIPE, check=True)
 
         line = p.stderr.splitlines()[-1]
         field = line.split(b"|")[-2].strip()
diff --git a/pyproject.toml b/pyproject.toml
index 2c032fd4d8dea..70bed7d9aeff9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -146,7 +146,6 @@ disable = [
   "self-assigning-variable",
   "self-cls-assignment",
   "signature-differs",
-  "subprocess-run-check",
   "super-init-not-called",
   "try-except-raise",
   "undefined-loop-variable",
diff --git a/scripts/run_autotyping.py b/scripts/run_autotyping.py
index f537b8d16c77a..032f742200a07 100644
--- a/scripts/run_autotyping.py
+++ b/scripts/run_autotyping.py
@@ -28,6 +28,7 @@ def main(argv: Sequence[str] | None = None) -> None:
             *args.paths,
             "--aggressive",
         ],
+        check=True,
     )
     sys.exit(output.returncode)
 
diff --git a/scripts/validate_docstrings.py b/scripts/validate_docstrings.py
index cbf02bc0a0156..a86630eba7d5d 100755
--- a/scripts/validate_docstrings.py
+++ b/scripts/validate_docstrings.py
@@ -211,7 +211,7 @@ def validate_pep8(self):
             file.write(content)
             file.flush()
             cmd = ["python", "-m", "flake8", "--quiet", "--statistics", file.name]
-            response = subprocess.run(cmd, capture_output=True, text=True)
+            response = subprocess.run(cmd, capture_output=True, check=False, text=True)
             stdout = response.stdout
             stdout = stdout.replace(file.name, "")
             messages = stdout.strip("\n")