collection.php

<?php

    /**
    * Implements hook_entity_insert().
    *
    * We use this hook as it's called later than node_insert().
    */
    function HOOK_entity_insert($node, $type) {
      module_field_collection_stuff($node, $type);
    }
    /**
    * Implements hook_entity_update().
    */
    function HOOK_entity_update($node, $type) {
      module_field_collection_stuff($node, $type);
    }

    /**
    * Do your magic
    */
    function module_field_collection_stuff($node, $type) {
      if ($type != 'node' || $node->type != 'my_content_type') {
        return;
      }

      // Create a dummy node so we can update the real node without
      // triggering all the node fields hooks.
      $update = new stdClass();
      $update->nid = $node->nid;
      $update->type = $node->type;
      $update->status = $node->status;
      $update->language = $node->language;

      $values['field_name'] = 'field_collection_field';
      $values['field_item_first'][LANGUAGE_NONE][0]['value'] = 'value';
      $values['field_item_second'][LANGUAGE_NONE][0]['value'] = 'second';

      // Create new field collection item.
      $field_collection_item = entity_create('field_collection_item', $values);

      // Attach it to the  node
      $field_collection_item->setHostEntity('node', $update, LANGUAGE_NONE, true);
      // Save field-collection item, without trigger the nodes own save.
      // This is because you might want to insert multiple field collection items.
      $field_collection_item->save(TRUE);

      // Update the fields.
      field_attach_presave('node', $update);
      field_attach_update('node', $update);
    }