Choose the AJAX pagination style for your Woocommerce shop among the AJAX-driven page numbers, Infinite Scroll, or next page loads triggered by the “Load more” button. “Default” will leave your theme pagination as is.

Ajax pagination will also work on pages with [products] shortcodes registered for filtering provided that there is only one shortcode-created products list on page.

Read about adding the native Woocommers pagination containers, or additional theme pagination containers in the Add to product list template section of plugin documentation.