That depends the value you want to store.
If the post can only have one term in the custom taxonomy, or you want to overwrite any terms already assigned to the post, the you can use an ACF taxonomy field.
On the other hand, if you want to append the term to the other terms already assigned to the post the you need to use acf/save_post and call wp_set_post_terms() https://developer.wordpress.org/reference/functions/wp_set_post_terms/ with $append set to true.
