The improvements in connectivity and data availability enable to fully integrate all the components of a production system. Manufacturing processes are frequently reconfigured over time, due to changes in lot sizes, process parameters and product customization. Despite this, warehousing operations are often disregarded: usually, automation systems for warehouses are set-up during the installation and their management is hardly ever reviewed. As a consequence, the manufacturing process is adapted to the capabilities of the warehousing system, rather than the other way round. To overcome this issue, this paper aims to propose a method capable to support an easy reconfiguration of warehousing operations based on the current state of the manufacturing process. The method is applied to an Autonomous Vehicle Storage and Retrieval Systems (AVS/RS), one of the most recent and promising automation technologies for warehouses. The proposed approach is based on both discrete-event simulation and analytical techniques and is applied to a real case of an Italian company. (C) 2018 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/)