diff --git a/autoapi/extension.py b/autoapi/extension.py
index 6c114130..aeb6f50e 100644
--- a/autoapi/extension.py
+++ b/autoapi/extension.py
@@ -141,6 +141,10 @@ def run_autoapi(app):
         if app.config.autoapi_generate_api_docs:
             sphinx_mapper_obj.output_rst(source_suffix=out_suffix)
 
+    # This function cannot be pickled into the Sphinx cache, so clear it.
+    # We won't need access to it again until a full rebuild is done anyway.
+    app.config.autoapi_prepare_jinja_env = None
+
 
 def build_finished(app, exception):
     if not app.config.autoapi_keep_files and app.config.autoapi_generate_api_docs:
diff --git a/docs/changes/445.bugfix b/docs/changes/445.bugfix
new file mode 100644
index 00000000..31230ea5
--- /dev/null
+++ b/docs/changes/445.bugfix
@@ -0,0 +1 @@
+Fix unpickable configuration value warning when using autoapi_prepare_jinja_env
\ No newline at end of file