The Science, Business and Policy Program (SBP) of the University of Groningen has been a work-based learning program for science master students since two decades. This program, a direct consequence of the Bologna declaration of education in Europe, has a distinctive position in European science curricula. Here, we use a web-based survey (N = 242), comparing alumni perceptions on the SBP program (N = 111) with a research oriented master (ROM, N = 131). Alumni from both programs predominantly had a content-driven motivation to choose for either the ROM or SBP format. For SBP alumni, this preference was also inspired by the master's focus on society and a career outside academia. We assessed self-perceived learning outcomes using an extended version of the Science Student Skills Inventory. Both groups were positive about the academic level of their program. Scientific content knowledge and practical research skills were perceived as sufficient by both groups, although significantly higher in the ROM group. Both groups were equally positive about obtained skills in academic reasoning and would have preferred more disciplinary content knowledge. The SBP group perceived their skills on teamwork, multidisciplinary working, leadership, ethical thinking and project work to be significantly higher compared to ROM alumni. The SBP group felt significantly more prepared for a career outside academia and the ROM group for a career in academia. Relatively the ROM group missed career preparation. Both specific work-based learning and classical research approaches were seen as valid ways to obtain a high-quality, science master level, although for different career ambitions.