Research informed by individuals’ lived experiences is a critical component of participatory research and nursing interventions for health promotion. Yet, few examples of participatory research in primary care settings with adolescents and young adults exist, especially with respect to their sexual health and health-risk behaviors. Therefore, we implemented a validated patient-centered clinical assessment tool to improve the quality of communication between youth patients and providers, sexual risk assessment, and youths’ health-risk perception to promote sexual health and reduce health-risk behaviors among adolescents and young adults in three community health clinic settings, consistent with national recommendations as best practices in adolescent health care. We describe guiding principles, benefits, challenges, and lessons learned from our experience. Improving clinical translation of participatory research requires consideration of the needs and desires of key stakeholders (e.g., providers, patients, and researchers) while retaining flexibility to successfully navigate imperfect, real-world conditions.