Background: Youth of color from low-income urban communities are crucial participants in research, as their involvement can shape effective, culturally responsive interventions and policy to promote youth health and well-being. These young people, however, are an often-neglected research population, due in part to perceived challenges associated with their inclusion as well as marginalized communities' justifiable mistrust of research. Objectives: Based on our experience conducting a school-based randomized intervention trial in Baltimore, Maryland, we present strategies for conducting research with low-income, urban youth of color. We discuss strategies in three domains: university-community partnership development, participant recruitment, and participant retention. Methods: We reviewed partnership building and recruitment strategies employed by our team across four years of trial implementation and evaluated success of participant retention at our final survey timepoint. Results: Partnership building was facilitated by selection of a study design that maximized benefits for all participants, promotion of capacity building at partner institutions, and attention to research staff hiring and training practices. Effective study recruitment strategies included personal contact with parents and close cooperation between school personnel and study staff. Providing incentives and collecting multiple types of participant contact information contributed to increased retention rates. On average, those who participated in the final survey timepoint were less likely to be male and Latinx and exhibited more favorable baseline mental health than those who did not, suggesting differential attrition based on youth characteristics. Conclusions: Lessons learned from this school-based trial can be applied more broadly to research with low-income urban youth of color. Researchers should strive to maximize scientific rigor, minimize harm to vulnerable adolescents and their communities, promote positive research experiences for young people, and provide concrete benefits to those who participate.