In an era of significant biomedical advances in the treatment of HIV, health disparities still persist. The participation of minority researchers brings new perspectives to health-disparities research. Mentoring is key to this process. We present the multifaceted mentoring model that evolved in the Puerto Rico Comprehensive Center for the Study of HIV Disparities and the Mentoring Institute for HIV and Mental Health. The model includes (1) multi-institutional collaborations, (2) competency development, and (3) cross-disciplinary teams. These aspects of the model provide guidelines for institutions seeking to formalize mentoring programs while addressing the complexities of health disparities. The competency development component is a powerful tool in assessing and supporting the researchers. Further explorations on the applicability of the model are encouraged.