Given the growth of cleanroom manufacturing for high-tech products and the high costs of operating within a cleanroom environment, an accompanying efficient manufacturing system is important. While abundant examples of efficient assembly manufacturing systems exist today, implementation of these into a sensitive cleanroom manufacturing environment has proven to be difficult. Against this background, this paper presents a transferable methodology to support the design of cleanroom assembly workstations which brings together aspects like cleanliness, ergonomics, modularity/flexibility and flow in an integrated manner. A set of guidelines was developed and embedded into a systematic procedure. The methodology was implemented and validated in a case at a high-tech precision manufacturing company, with high-mix-low-volume characteristics. The case study underlines the feasibility of the approach and the multicriterial improvement of workstation design towards the current state of the art. It also lead to a transferable cleanroom workstation design.