diff --git a/test/mavsdk_tests/process_helper.py b/test/mavsdk_tests/process_helper.py
index 587cc7f9ec..513abbb726 100644
--- a/test/mavsdk_tests/process_helper.py
+++ b/test/mavsdk_tests/process_helper.py
@@ -176,15 +176,24 @@ class Px4Runner(Runner):
     def clear_rootfs(self) -> None:
         rootfs_path = self.cwd
         if self.verbose:
-            print("Deleting rootfs: {}".format(rootfs_path))
-        if os.path.isdir(rootfs_path):
-            shutil.rmtree(rootfs_path)
+            print("Clearing rootfs (except logs): {}".format(rootfs_path))
+        for item in os.listdir(rootfs_path):
+            if item == 'log':
+                continue
+            path = os.path.join(rootfs_path, item)
+            if os.path.isfile(path) or os.path.islink(path):
+                os.remove(path)
+            else:
+                shutil.rmtree(path)
 
     def create_rootfs(self) -> None:
         rootfs_path = self.cwd
         if self.verbose:
             print("Creating rootfs: {}".format(rootfs_path))
-        os.makedirs(rootfs_path)
+        try:
+            os.makedirs(rootfs_path)
+        except FileExistsError:
+            pass
 
 
 class GzserverRunner(Runner):