While social programs are often assessed using short-term impact studies, longitudinal designs allow evaluators to capture change over time, identify longer-term outcomes, adapt instruments, and better understand participants in transition. A mixed methods design can be critical in understanding these dynamics; yet there is a lack of literature exploring the practical considerations of planning and conducting qualitative and quantitative data collection and analysis within longitudinal studies. This paper examines two different mixed methods frameworks used in a 5-year evaluation of three youth entrepreneurship programs in East Africa. We show how the evaluation team dealt with unique challenges across methods and over time, and how the design ultimately facilitated a richer understanding of program impacts and processes. Considerations for conducting this type of study are explored, related to the impact of longevity on analysis and research staff. Successfully using a longitudinal mixed methods approach requires researchers to be strategic and reflexive, and work in close collaboration.