diff --git a/src/_pytest/config/__init__.py b/src/_pytest/config/__init__.py
index f7c4de5d7e9..fd24f2718c6 100644
--- a/src/_pytest/config/__init__.py
+++ b/src/_pytest/config/__init__.py
@@ -1587,8 +1587,12 @@ def issue_config_time_warning(self, warning: Warning, stacklevel: int) -> None:
         config_filters = self.getini("filterwarnings")
 
         with warnings.catch_warnings(record=True) as records:
+            existing_filters = warnings.filters[:]
             warnings.simplefilter("always", type(warning))
             apply_warning_filters(config_filters, cmdline_filters)
+            for f in existing_filters:
+                if f not in warnings.filters:
+                    warnings.filters.append(f)
             warnings.warn(warning, stacklevel=stacklevel)
 
         if records: