Growing evidence has come to suggest that model-based inquiry can improve student learning outcomes and attitudes toward STEM in the biological sciences and beyond. In our introductory biology laboratory course that focuses on cellular and molecular biology, we introduced model-based inquiry (MBI) labs to create a more student-focused course that provides a robust opportunity for students to learn about the research process itself. Prior to the intervention, our laboratory course was designed as a set of traditional lab classes. From 2019 to 2022, we implemented three iterations of the MBI lab structure. In order to assess learning and changes in attitudes toward science, we implemented a pre-course and post-course test that assessed knowledge of experimental design and graph analysis as well as students' attitudes toward science. Our data indicate that the modifications to the course maintained the level of learning gains seen in the traditional labs. One of the major challenges we encountered was the onset of the COVID-19 pandemic during 2020, in the middle of the data collection period, just after our first iteration of the MBI labs. Upon return to regular room capacity and teaching schedules, we continued with further iterations of the MBI lab approach, however, impacts of COVID-19 to student learning likely persisted (and may continue to persist in the coming years). Despite the challenges to student learning, we did not find evidence of a decrease in learning gains. While further data are needed to fully assess the impact of MBI, our results suggest that the MBI labs may hold promise as a resilient structure on which to build student learning. Interviews with students also showed that feelings were overwhelmingly positive about the labs and the teamwork, but there was added stress when lab activities did not go according to plan. Altogether, our findings suggest that MBI may support laboratory and critical thinking skills while promoting self-efficacy in undergraduate students.