Innovations in agricultural technology promise to tackle today’s sustainability challenges. However, the development of such innovations typically lacks comprehensive evaluation of their sustainability. Thus, the technologies are potentially not aligned with current sustainability goals. Microalgae are an example of such an innovation, particularly their use as feedstuff. Drawing on data of two laboratory-scale photobioreactors (glass and polymethylmetacrylate), we evaluated the sustainability of microalgae production as alternative feedstuff in Switzerland. Methodological improvements were identified, and participation of stakeholders helped to enhance the comprehensiveness and evaluate the usefulness of such assessments. The ratio of the environmental impacts between both photobioreactors were between 4% and 35% except for water scarcity where the difference reached 65%. The social and economic indicators were comparable between both reactors. In both cases, the electricity input contributed most to the environmental impacts. Community engagement was an important social indicator. Neither of the photobioreactors were economically sustainable, which can be due to the laboratory scale to some extent, suggesting that future economic assessments need to be more refined and upscaled. A final stakeholder workshop confirmed the need for such assessments and highlighted limitations to be addressed in future studies: (1) the development of better methods for prospective sustainability assessments, (2) comprehensive stakeholder inclusion and corresponding resources planning, and (3) the careful evaluation of the sustainability of reference systems.