diff --git a/lisa/_kmod.py b/lisa/_kmod.py
index 7c767dd5af833806180ba60b293e458a173e6c5d..40afb2f9f09e3ccc2092e1dcd569dfafe75a344e 100644
--- a/lisa/_kmod.py
+++ b/lisa/_kmod.py
@@ -120,7 +120,6 @@ import re
 import functools
 import bisect
 import threading
-import hashlib
 import itertools
 import logging
 import datetime
@@ -817,6 +816,7 @@ class KernelTree(Loggable, SerializeViaConstructor):
 
     @classmethod
     def _prepare_tree(cls, path, make_vars, build_env, apply_overlays, overlay_backend):
+        path = Path(path)
         logger = cls.get_logger()
         _make_vars = [
             f'{name}={val}'
@@ -853,6 +853,26 @@ class KernelTree(Loggable, SerializeViaConstructor):
 
         bind_paths = {path: path}
 
+        def fixup_kernel_tree():
+            # TODO: re-assess
+
+            # The headers in /sys/kheaders.tar.xz generated by
+            # CONFIG_IKHEADERS=y are broken since kernel/gen_kheaders.sh strip
+            # some comments from the file. KBuild then proceeds on checking the
+            # checksum and the check fails. This used to be a simple warning,
+            # but has now been turned into an error in recent kernels.
+            # We remove the SHA1 from the file so that the check is skipped.
+            for _path in (path / 'include' / 'linux' / 'atomic').iterdir():
+                content = _path.read_bytes()
+                lines = [line for line in content.split(b'\n') if line]
+                if lines and lines[-1].lstrip().startswith(b'//'):
+                    # Remove the last line, containing the sha1
+                    content = b'\n'.join(lines[:-1]) + b'\n'
+                    sha1 = hashlib.sha1(content).hexdigest()
+                    content += b'// ' + sha1.encode('ascii') + b'\n'
+                    _path.write_bytes(content)
+
+
         if build_env == 'alpine':
             @contextlib.contextmanager
             def cmd_cm(cmds):
@@ -874,11 +894,14 @@ class KernelTree(Loggable, SerializeViaConstructor):
             # Apply the overlays before running make, so that it sees the
             # correct headers and conf etc
             apply_overlays()
+            fixup_kernel_tree()
 
             _subprocess_log(post, logger=logger, level=logging.DEBUG)
+
             # Re-apply the overlays, since we could have overwritten important
             # things, such as include/linux/vermagic.h
             apply_overlays()
+            fixup_kernel_tree()
 
 
     @classmethod