Engineer-to-order manufacturing, characterized by highly customized products and complex workflows, presents unique challenges for warehouse management and operational efficiency. This paper explores the potential of a digital twin as a transformative solution for engineer-to-order environments in manufacturing companies realizing prefabricated building components. This paper outlines a methodology encompassing users’ requirements and the design to support the development of a digital twin that integrates Internet of Things devices, Building Information Modeling, and artificial intelligence capabilities. It delves into the specific challenges of outdoor warehouse optimization and worker safety within the context of engineer-to-order manufacturing, and how the digital twin aims to address these issues through data collection, analysis, and visualization. The research is conducted through an in-depth analysis of the warehouse of Focchi S.p.A., a leading manufacturer of high-tech prefabricated building envelopes. Focchi’s production processes and stakeholder interactions are investigated, and the paper identifies key user groups and their multiple requirements for warehouse improvement. It also examines the potential of the digital twin to streamline communication, improve decision-making, and enhance safety protocols. While preliminary testing results are not yet available, the paper concludes by underlining the significant opportunities offered by a BIM-, IoT-, and AI-powered digital twin for engineer-to-order manufacturers. This research, developed within the IRIS project, serves as a promising model for integrating digital technologies into complex warehouse environments, paving the way for increased efficiency, safety, and ultimately, a competitive edge in the market of manufacturing companies working in the construction industry.