Digital twin technology is currently underutilized in the agro-industrial sector. Therefore, implementing an adequate digital twin model will enable a reduction in production line design costs and facilitate the identification of potential vulnerabilities that may arise during the manufacturing process. Consequently, the aim of this research is to develop a methodology for creating a digital twin of a cheese production line based on virtual reality technology. In alignment with the stated goal, the paper proposes a methodology for designing the production line using virtual reality technology, presented as a three-stage strategy: allocation of roles for virtual reality users, task assignment, and system design. The system design stage encompasses 3D equipment model design, model import, scene creation, and system testing. The object of the study, existing equipment, and utilized software are described. The stages of 3D modeling are presented, involving the creation of a geometric model, texture application, and 3D visualization. Parameters adjustable through the virtual reality platform’s integrated editing methods are outlined. During the scene creation stage, interaction tasks performed during the virtual reality walkthrough are presented: “look and walk”, “touch and teleport”, and “grab”. Furthermore, three additional specific functions are introduced: “virtual menu”, “ voice-over training”, and “production process animation”. To evaluate the proposed approach, a user survey was conducted, which confirmed the necessity of applying a digital twin, developed using virtual reality technology, for the design of cheese production lines. Conclusions were drawn from the conducted research, and further directions for development are proposed.