The intelligent automated store warehouse (iZMS) research and development project was created to meet the expectations of a modern automatic store. The project concerns the development of the concept and pilot implementation of an automated store warehouse adapted to the autonomous and automatic sales of goods selected by retail chains. One of the aims of the iZMS project is to develop a scalable solution that allows for the simple adaptation of the iZMS to the needs of a potential customer, taking into account their requirements in terms of the quantity and variety of assortment offered within the iZMS. An important requirement in the use of the iZMS system is minimizing the customer waiting time for purchased products. This problem is related, among others, to the placement of products on the shelves of racks and will be solved in the optimizing process. Running optimization tasks requires a simulator that will mimic the features of a physical device faster than in real time in order to generate many proposals of the allocation of goods on storage racks in the shortest possible time and choose the best one, guaranteeing the shortest picking time of a representative basket of goods. A numerical simulator was developed to model the physical structures of food storage equipment and then simulate the sales process. Among the results obtained, the most important are the time parameters of individual operations, which will ultimately be used to optimize the placement of goods on storage racks. After analyzing the needs resulting from the usage of the iZMS system, we decided to develop a dynamic, deterministic simulator with discrete objects and perform the simulation with a controlled time increment and, in some cases, to utilize elements of event-driven simulation, in which the flow of goods is simulated with first-in, first-out (FIFO) queues. Finally,verification of the numerical simulator with a physical model confirmed that it can be employed in optimization processes.