Our case study is on an ongoing research program examining adolescent socio-emotional and science, technology, engineering, and mathematics development as part of participation in an afterschool program. We briefly discuss the research context, before discussing how the research study evolved and was implemented. Attention is directed toward the challenges that arose during the research. Practical lessons learned from this and our other related studies are then presented. Throughout the case study, we use the specifics of the presented research study to discuss general issues related to conducting community-based mixed-method longitudinal research with adolescents.