This paper represents the second contribution from an action research study on a bachelor-level quantum chemistry and spectroscopy course. In the proposed instructional model, active learning principles are extended outside lectures to form a student-centred course structure. The new model resulted in superior learning outcomes compared to a class where active learning elements were limited to course lectures, as demonstrated by previous research. In this article, I try to understand this improvement through an analysis of student motivation and experiences in the framework of self-determination theory. Based on my analysis of student feedback data and interviews, tasks that facilitated direct interaction with peers or course staff were seen as key factors in enhancing learning and motivation. In addition, the presence of various interconnected course components that supported students at different stages of the learning process was experienced as central to learning. Together, these two publications demonstrate that the incorporation of active learning principles outside lectures can substantially improve both learning and motivation.