diff --git a/test/mavsdk_tests/mavsdk_test_runner.py b/test/mavsdk_tests/mavsdk_test_runner.py
index 9c8148b33b..4360202070 100755
--- a/test/mavsdk_tests/mavsdk_test_runner.py
+++ b/test/mavsdk_tests/mavsdk_test_runner.py
@@ -3,7 +3,6 @@
 import argparse
 import datetime
 import fnmatch
-import glob
 import json
 import math
 import os
@@ -326,8 +325,6 @@ class Tester:
     def run_test_case(self, test: Dict[str, Any],
                       case: str, log_dir: str) -> bool:
 
-        self.clear_params()
-
         self.start_runners(log_dir, test, case)
 
         logfile_path = self.determine_logfile_path(log_dir, 'combined')
@@ -369,15 +366,6 @@ class Tester:
                 print("  - {}".format(runner.get_log_filename()))
         return is_success
 
-    def clear_params(self) -> None:
-        param_files = glob.glob(
-            "build/px4_sitl_default/tmp/rootfs/eeprom/parameters_*",
-            recursive=False)
-        for param_file in param_files:
-            if self.verbose:
-                print("Deleting param file: {}".format(param_file))
-            os.unlink(param_file)
-
     def start_runners(self,
                       log_dir: str,
                       test: Dict[str, Any],
diff --git a/test/mavsdk_tests/process_helper.py b/test/mavsdk_tests/process_helper.py
index 1f3a205071..5c35a20d40 100644
--- a/test/mavsdk_tests/process_helper.py
+++ b/test/mavsdk_tests/process_helper.py
@@ -5,6 +5,7 @@ import time
 import os
 import atexit
 import subprocess
+import shutil
 import threading
 import errno
 from typing import Any, Dict, List, TextIO, Optional
@@ -139,7 +140,8 @@ class Px4Runner(Runner):
         super().__init__(log_dir, model, case, verbose)
         self.name = "px4"
         self.cmd = workspace_dir + "/build/px4_sitl_default/bin/px4"
-        self.cwd = workspace_dir + "/build/px4_sitl_default/tmp/rootfs"
+        self.cwd = workspace_dir + \
+            "/build/px4_sitl_default/tmp_mavsdk_tests/rootfs"
         self.args = [
                 workspace_dir + "/build/px4_sitl_default/etc",
                 "-s",
@@ -151,6 +153,8 @@ class Px4Runner(Runner):
         self.env["PX4_SIM_MODEL"] = self.model
         self.env["PX4_SIM_SPEED_FACTOR"] = str(speed_factor)
         self.debugger = debugger
+        self.clear_rootfs()
+        self.create_rootfs()
 
         if not self.debugger:
             pass
@@ -169,6 +173,19 @@ class Px4Runner(Runner):
             self.args = [self.cmd] + self.args
             self.cmd = self.debugger
 
+    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)
+
+    def create_rootfs(self) -> None:
+        rootfs_path = self.cwd
+        if self.verbose:
+            print("Creating rootfs: {}".format(rootfs_path))
+        os.makedirs(rootfs_path)
+
 
 class GzserverRunner(Runner):
     def __init__(self,