functions.php

<?php

/**
 * Custom posts per page
 *
 */
function be_posts_per_page( $query ) {
  
  // Only run on archive pages 
  if( ! $query->is_main_query() || is_admin() || ! ( $query->is_home() || $query->is_archive ) )
      return;
  
  $posts_first_page = 3;
  $posts_per_page = 9;
  $page = $query->query_vars['paged'];
  
  // First Page
  if( ! $page ) {
    $query->set( 'posts_per_page', $posts_first_page );

  // Other Pages
  } else {
    $query->set( 'posts_per_page', $posts_per_page );
    $query->set( 'offset', $posts_first_page + $posts_per_page * ( $page - 2 ) );
  }
}
add_action( 'pre_get_posts', 'be_posts_per_page' );