Advanced therapy medicinal products (ATMP) represents a new class of medicinal products, which include - amongst others - somatic cell and gene therapies. As the final product is intended for administration into humans, manufacturers of ATMPs are obligated to apply good manufacturing practice (GMP) standards within their processes. Reaching and maintaining such standards is cost intensive and requires sophisticated manufacturing facilities. As a result, academic researchers who are developing these novel therapeutic approaches are facing new technological and financial challenges. In order to bring more commercially accessible therapies to patients and demonstrate efficient manufacturing technologies, we established the clean-room technology assessment technique (CTAT). CTAT comprises several tools to identify and assign a reliable monetary value to the different operational processes. The model also serves as a guideline for optimizing the operation of an academic GMP facility.