diff --git a/test/mavsdk_tests/mavsdk_test_runner.py b/test/mavsdk_tests/mavsdk_test_runner.py
index 8bcc3e083a..b0ba4a8134 100755
--- a/test/mavsdk_tests/mavsdk_test_runner.py
+++ b/test/mavsdk_tests/mavsdk_test_runner.py
@@ -341,6 +341,8 @@ class Tester:
             is_success = False
 
         self.stop_runners()
+        # Collect what was left in output buffers.
+        self.collect_runner_output()
         self.stop_combined_log()
 
         result = {'success': is_success,
diff --git a/test/mavsdk_tests/process_helper.py b/test/mavsdk_tests/process_helper.py
index 0408ec154e..761fc32e41 100644
--- a/test/mavsdk_tests/process_helper.py
+++ b/test/mavsdk_tests/process_helper.py
@@ -53,7 +53,7 @@ class Runner:
             cwd=self.cwd,
             env=self.env,
             stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
+            stderr=subprocess.PIPE,
             universal_newlines=True
         )
 
@@ -63,11 +63,12 @@ class Runner:
 
     def process_output(self) -> None:
         assert self.process.stdout is not None
-        while not self.stop_thread.is_set():
+        while True:
             line = self.process.stdout.readline()
-            if line == "\n":
-                continue
-            if not line:
+            if not line and \
+                    (self.stop_thread.is_set() or self.poll is not None):
+                break
+            if not line or line == "\n":
                 continue
             self.output_queue.put(line)
             self.log_fd.write(line)
@@ -99,8 +100,6 @@ class Runner:
         if not self.stop_thread:
             return 0
 
-        self.stop_thread.set()
-
         returncode = self.process.poll()
         if returncode is None:
 
@@ -123,8 +122,8 @@ class Runner:
             print("{} exited with {}".format(
                 self.cmd, self.process.returncode))
 
+        self.stop_thread.set()
         self.thread.join()
-
         self.log_fd.close()
 
         return self.process.returncode