ABSTRACT This paper explores the practice of participatory design (PD) in the process of designing functionally and technically complex buildings, exemplified through the case study of the Faculty of Mathematics and Natural Sciences in Pristina (Kosovo), a building that conducts and promotes scientific discoveries. Functional complexity refers to the number and diversity of functions the building needs to accommodate, while technical complexity refers to the degree of sophistication and intricacy in the building's systems and components. Participatory design can be a valuable design approach in designing complex buildings. The case of the Faculty of Mathematics and Natural Sciences in Pristina (Kosovo) is an example of how PD can be transformed into an instrument of understanding the complexity of the building by promoting a user-focused design approach and helping in designing the tools of involvement depending on the goals to be achieved. Briefing workshop, design game and choice catalogue were methods that were used while a variety of tools were designed during the design stages; some were adaptations of existing PD tools and others were designed especially for this case. The participants included a diverse ‘multiple community’ of stakeholders, comprising end users (students, professors and administrative staff), strategic partners (client, investor, project manager and executives) as well as the technical working group (engineers and technical experts). The results demonstrate PD’s transformative potential into a structured instrument for understanding, analysing and preventing mistakes in the design of complex buildings.