Comrogen includes support for multiple warehouses and inventories. This allows admins to set up inventory and availability per product and per warehouse. Each warehouse/inventory may have different pricing including: sale, cost, msrp, map as well as customer level pricing.

Products may be setup to have a default warehouse and secondary suplementaries warehouses; if a product is available from multiple warehouses, display providers can be customized to give customers the option to choose the location from where they would like the item to ship from. With plugins, this functionality may be extended to allow customers to shop from their local store based on a zip/shipping code; the site will display only products that are available in their local region.

Comrogen includes tight integration between the warehouse sub system and the product, product group, shipping, and checkout systems. This allows admins to tailor how the order is fulfilled e.g. special shipping discounts when orders are being shipped from multiple warehouses, or restricting orders to a single warehouse for easier order management.

The warehouse system includes support for distributor notification and integration (via plugins). This allows the system to notify distributors to ship products when products are ordered. Many websites use drop-ship and JIT (just-in-time) fulfillment solutions using email; Comrongen includes support for this and extends distributor integration by also offering XML, JSON, EDI, and REST to relay order information.