The purpose of our action research project was to improve students’ motivation in a multi-section introductory neuroscience laboratory course. In this paper, we present: (a) how we collected data related to students’ motivation and engagement, (b) how we analyzed and used the data to make modifications to the courses, (c) the results of the course modifications, and (d) some possible explanations for our results. Our aim is not only to provide the results of our study, but also to explain the process that we used, with the hopes that other instructors can use similar approaches to improve students’ motivation in their courses. Our attempts to improve students’ motivation-related perceptions were successful in some instances, but not in others. Of particular note was our finding that some of the students’ perceptions varied even though the course syllabus was the same across sections. We attributed this variation to the learning environment developed by the teaching assistants (TAs) who taught the different sections. We provide some strategies that faculty instructors can use to redesign courses with high enrollments and help TAs motivate their students.