Matter and Interactions (M&I) has recently been adopted as a novel introductory physics course that focuses on the application of a small number of fundamental physical principles to the atomic and molecular nature of matter. This study investigated how five physics teaching assistants (TAs) developed professional knowledge for teaching from their teaching experiences. Specifically, we explored what experiences influenced their knowledge development for teaching the innovative introductory physics course, M&I. Through a qualitative, multiple case study research design, data was collected from multiple sources: non-participant observations, digitally recorded video, semistructured interviews, TAs' written reflections, and researchers' field notes. As TA's progressed through the semester, two experiences emerged as having a significant role in their development of knowledge for teaching M&I: (1) setting teaching, learning, and curriculum goals for their classes; and (2) encountering dilemmas of teaching and learning. The results of this study will contribute to future preparation of the innovative introductory physics course as well as other college level science courses.