Research seeking to understand and improve social conditions for marginalized youth would benefit from merging complex mixed methods research designs emphasizing multilevel data and participatory social justice principles. We contribute to mixed methods research by introducing a novel framework that accomplishes this task and by illustrating its real-world application via "PhotoStories," a multistage study aimed at understanding youths' community-based experiences and emotional well-being. During the project's three phases (preparation, training, and dissemination) we obtained and integrated quantitative and qualitative data at multiple ecological levels. Additionally, we examined youth perceptions about their participation, an important outcome given our focus on participatory social justice. We also provide lessons learned and recommendations for investigators seeking to use a similar approach for youth-focused research.