diff --git a/test/functional/test_framework/test_framework.py b/test/functional/test_framework/test_framework.py
--- a/test/functional/test_framework/test_framework.py
+++ b/test/functional/test_framework/test_framework.py
@@ -284,7 +284,18 @@
             self.log.error("Hint: Call {} '{}' to consolidate all logs".format(os.path.normpath(
                 os.path.dirname(os.path.realpath(__file__)) + "/../combine_logs.py"), self.options.tmpdir))
             exit_code = TEST_EXIT_FAILED
-        logging.shutdown()
+        # Logging.shutdown will not remove stream- and filehandlers, so we must
+        # do it explicitly. Handlers are removed so the next test run can apply
+        # different log handler settings.
+        # See: https://docs.python.org/3/library/logging.html#logging.shutdown
+        for h in list(self.log.handlers):
+            h.flush()
+            h.close()
+            self.log.removeHandler(h)
+        rpc_logger = logging.getLogger("BitcoinRPC")
+        for h in list(rpc_logger.handlers):
+            h.flush()
+            rpc_logger.removeHandler(h)
         if cleanup_tree_on_exit:
             shutil.rmtree(self.options.tmpdir)
         return exit_code