Create taxonomy with rewrite with Post types creator https://github.com/pelmered/post-types-creator

taxonomies.php

<?php
if( class_exists( 'PE_Post_Type_Creator' ) )
{
    $ptc = new PE_Post_Type_Creator();
    $text_domain = 'text-domain';

    $ptc->set_taxonomies(array(

        'min-taxonomi' => array(
            'singular_label' => _x('Min taxonomi', 'Post type plural', $text_domain),
            'plural_label'  => _x('Mina taxonomier', 'Post type singular', $text_domain),
            'description'   => _x('beskrivning', 'Post type description', $text_domain),
            'post_type'    => 'product',

            // Override any defaults in register_taxonomy()
            // http://codex.wordpress.org/Function_Reference/register_taxonomy
            'rewrite' => array(
                'slug'         => '/shop/min-taxonomi',
                'with_front'   => false
            ),
        ),

        'min-taxonomi-2' => array(
            'singular_label' => _x('Min andra taxonomi', 'Post type plural', $text_domain),
            'plural_label'  => _x('Mina andra taxonomier', 'Post type singular', $text_domain),
            'description'   => _x('beskrivning', 'Post type description', $text_domain),
            'post_type'    => 'product',

            // Override any defaults in register_taxonomy()
            // http://codex.wordpress.org/Function_Reference/register_taxonomy
            'rewrite' => array(
                'slug'         => '/shop/min-taxonomi2',
                'with_front'   => false
            ),
        ),

    ));

    add_action( 'init', array($ptc, 'init'), 0 );
}