Multiple attribute selection sets
I figured this out myself..

So the basic idea is that we build the form based on the setting of $form_state['num_names']. The custom submit functions for the "add more" button increment and decrement $form_state['num_names'] and then force a rebuild of the form.
We then iterate over the fields for the product and search for entity reference fields to a commerce option set.
(This takes into account that the commerce_product_option module has been properly configured and option sets have been set.)
We create a new blank option set each time and add a quantity field with an extra key to attach it with the current option set.

For the submit callback,i had to dig deeper into the module and tweaked a bit for these specific attributes.

&lt;?php

 function multiple_option_sets_form_alter(&amp;$form, &amp;$form_state, $form_id) {
if ((strpos($form_id, 'commerce_cart_add_to_cart_form_') &gt; -1)) {
    multiple_option_sets_add_more_form($form, $form_state, $form_id);
    $form['#submit'][] = 'multiple_option_sets_add_more_submit';
}

}

function multiple_option_sets_add_more_form(&amp;$form, &amp;$form_state, $form_id) {

$form['field_extra_attributes']['#prefix'] = '&lt;div id="ajax-attributes-wrapper"&gt;';
$form['field_extra_attributes']['#suffix']= '&lt;/div&gt;';


// Build the fieldset with the proper number of names. We'll use
// $form_state['num_names'] to determine the number of textfields to build.
if (empty($form_state['num_names'])) {
    $form_state['num_names'] = 0;
}

for ($i = 0; $i &lt; $form_state['num_names']; $i++) {

    //lets add all the fields we want in the set
    // Because we have many fields with the same values, we have to set
    // #tree to be able to access them.
    $form['#tree'] = TRUE;


    // Get the current product. Is added in the cart module.
    if (isset($form_state['default_product'])) {
        $product_id = $form_state['default_product']-&gt;product_id;
    }
    elseif (isset($form_state['default_product_id'])) {
        $product_id = $form_state['default_product_id'];
    }
    elseif (isset($form_state['products'])) {
        $current_product = reset($form_state['products']);
        $product_id = $current_product-&gt;product_id;
    }
    else {
        return;
    }

    $current_product = commerce_product_load($product_id);

    $someFieldIsAdded = FALSE;

    // Iterates the fields of this product. We search for entity reference fields
    // to a commerce option set.
    foreach ($current_product as $field_name =&gt; $field) {
        $field_info = field_info_field($field_name);

        if ($field_info['type'] != 'entityreference' || !isset($field_info['settings']['target_type']) || $field_info['settings']['target_type'] != 'commerce_option_set') {
            continue;
        }

        // Do not display our options if this field has been marked as an attribute field.
        $field_instance_info = field_info_instance('commerce_product', $field_name, $current_product-&gt;type);
        if ($field_instance_info['commerce_cart_settings']['attribute_field']) {
            return;
        }

        $lang_code = field_language('commerce_product', $current_product, $field_name);
        if (!isset($field[$lang_code])) {
            continue;
        }

        // Create a new blank option set.

        foreach($field[$lang_code] as $key =&gt; $data) {

            $option_set = commerce_option_set_load($data['target_id']);

            $values = array(
            'set_id' =&gt; $option_set-&gt;set_id,
            );

            $option = commerce_option_new($values);

            $form_state['commerce_option'][$field_name][$key+1+$i]['option'] = $option;

            $form[$field_name][$key+1+$i] = array(
            '#parents' =&gt; array($field_name, $key+1+$i),
            );

            field_attach_form('commerce_option', $option, $form[$field_name][$key+1+$i], $form_state);
            $someFieldIsAdded = TRUE;

        }
    }

    $form['field_extra_attributes'][$i+1]['quantity'] = array(
    '#type' =&gt; 'textfield',
    '#title' =&gt; t('Quantity'),
    '#prefix' =&gt; '&lt;div class="col2"&gt;',
    '#suffix' =&gt; '&lt;/div&gt;'
    );

}

$form['actions']['add_more'] = array(
'#type' =&gt; 'submit',
'#value' =&gt; t('Add more'),
'#weight' =&gt; 50,
'#submit' =&gt; array('multiple_option_sets_add_more_add_one'),
'#ajax' =&gt; array(
'callback' =&gt; 'multiple_option_sets_add_more_callback',
'wrapper' =&gt; 'ajax-attributes-wrapper',
),
);

return $form;

}

/**
* Callback for both ajax-enabled buttons. 
*
* Selects and returns the fieldset with the names in it.
*/
function multiple_option_sets_add_more_callback($form, $form_state) {
return $form['field_extra_attributes'];
}

/**
* Submit handler for the "add-one-more" button.
*
* Increments the max counter and causes a rebuild.
*/
function multiple_option_sets_add_more_add_one($form, &amp;$form_state) {
$form_state['num_names']++;
$form_state['rebuild'] = TRUE;
}

/**
* Submit handler for the "remove one" button.
*
* Decrements the max counter and causes a form rebuild.
*/
function multiple_option_sets_add_more_remove_one($form, &amp;$form_state) {
if ($form_state['num_names'] &gt; 1) {
    $form_state['num_names']--;
}
$form_state['rebuild'] = TRUE;
}


function multiple_option_sets_commerce_cart_product_comparison_properties_alter(&amp;$comparison_properties) {
// Force separate line items when the same product is added to the cart from
// different display paths.
$comparison_properties[] = 'field_color';
}

/**
* Cart submit callback function. This is required to create / update
* the option related to the line item.
*
* @param $form Form array
* @param $form_state The form state array.
* @return void
*/
function multiple_option_sets_add_more_submit($form, $form_state){


// Get current product, taking into account different Commerce versions behavior.
if (isset($form_state['default_product'])) {
    $product_id = $form_state['default_product']-&gt;product_id;
}
elseif (isset($form_state['default_product_id'])) {
    $product_id = $form_state['default_product_id'];
}
elseif (isset($form_state['products'])) {
    $current_product = reset($form_state['products']);
    $product_id = $current_product-&gt;product_id;
}
else {
    return;
}

$current_product = commerce_product_load($product_id);

// Iterates the fields of this product. We search for entity reference fields
// to a commerce option set.
foreach ($current_product as $field_name =&gt; $field) {
    $field_info = field_info_field($field_name);

    if ($field_info['type'] != 'entityreference' || !isset($field_info['settings']['target_type']) || $field_info['settings']['target_type'] != 'commerce_option_set') {
        continue;
    }

    $lang_code = field_language('commerce_product', $current_product, $field_name);
    if (!isset($field[$lang_code])) {
        continue;
    }

    foreach ($form_state['values']['field_extra_attributes'] as $delta =&gt; $set_id) {

        $option = $form_state['commerce_option'][$field_name][$delta]['option'];

        // Notify field widgets and populate option with values.
        field_attach_submit('commerce_option', $option, $form[$field_name][$delta], $form_state);

        // Check if our option is empty. If yes we shouldn't save anything.
        // Cannot use field_get_items() because it calls field_language().
        $option_extracted = commerce_option_get_valuables($option);
        $ow = entity_metadata_wrapper('commerce_option', $option);
        $empty = TRUE;

        foreach (array_keys($option_extracted) as $option_field) {
            $value = $ow-&gt;$option_field-&gt;value();
            if (!empty($value)) {
                $empty = FALSE;
                break;
            }
        }

        if ($empty) {
            continue;
        }
        global $user;
        if($delta != 0) {
            $new_line_item = commerce_product_line_item_new($current_product, $form_state['values']['field_extra_attributes'][$delta]['quantity'], $form_state['line_item']-&gt;order_id, $form_state['line_item']-&gt;data, $form_state['line_item']-&gt;type);
            $new_line_item = commerce_cart_product_add($user-&gt;uid, $new_line_item);
            //var_dump($form_state['line_item']);
            //var_dump($new_line_item);
            //die();
            $line_item_id = $new_line_item-&gt;line_item_id;
        }
        else {
            $line_item_id = $form_state['line_item']-&gt;line_item_id;
        }
        $product_id = $current_product-&gt;product_id;
        $match = FALSE;

        // Check if the newly created options exist on this line item already.
        // If yes we needn't save anything, commerce will just increase the
        // quantity.
        $query = db_select('commerce_option', 'co')
        -&gt;fields('co', array('option_id'))
        -&gt;condition('line_item_id', $line_item_id, '=')
        -&gt;condition('product_id', $product_id, '=');

        $result = $query-&gt;execute()-&gt;fetchCol();

        if (!empty($result)) {
            $commerce_option_entities = commerce_option_load_multiple($result);
            $option_extracted = serialize($option_extracted);

            foreach ($commerce_option_entities as $commerce_option) {
                $commerce_option_extracted = commerce_option_get_valuables($commerce_option);
                $commerce_option_extracted = serialize($commerce_option_extracted);
                if ($commerce_option_extracted == $option_extracted) {
                    $match = TRUE;
                    break;
                }
            }
        }

        if ($match) {
            continue;
        }

        $option-&gt;line_item_id = $line_item_id;
        $option-&gt;product_id = $product_id;

        // Save the option.
        commerce_option_save($option);

    }
}
}
?&gt;