This study examines the potential of problem-based cooperative learning (PBCL) in expanding undergraduate physics students’ understanding of, and engagement with, the scientific process. Two groups of first-year physics students (n = 180) completed a questionnaire which compared their perceptions of learning science with their engagement in physics labs. One cohort completed a lab based on a PBCL approach, whilst the other completed the same experiment, using a more traditional, manual-based lab. Utilising a participant research approach, the questionnaire was co-constructed by researchers and student advisers from each cohort in order to improve shared meaning between researchers and participants. Analysis of students’ responses suggests that students in the PBCL cohort engaged more in higher-order problem-solving skills and evidenced a deeper understanding of the scientific process than students in the more traditional, manual-based cohort. However, the latter cohort responses placed more emphasis on accuracy and measurement in lab science than the PBCL cohort. The students in the PBCL cohort were also more positively engaged with their learning than their counterparts in the manual led group.