This study investigated the impact of collaborative and individualized student response system-based instruction on learner motivation, metacognition, and concept transfer in a large-enrolment undergraduate science course. Participants in the collaborative group responded to conceptual questions, discussed their responses in small groups, and provided a revised response to the question (peer instruction [PI]). A comparison group provided individualized responses (IRs) to the same questions. Results of the motivation measure revealed a drop in confidence for students in both groups. This may be explained by a significant increase in the knowledge of cognition in both IR and PI groups, which likely mediated a recalibration of confidence to a lower, yet more realistic level. A significant interaction was found between gender and student response system strategy relative to the regulation of cognition, revealing that females improved in the PI group, while males reported improvement in the regulation of cognition in the IR group. A custom instrument was developed to measure near and far concept transfer abilities. The PI group scored significantly higher on the test of near transfer than the IR group.