This article examines the methodological implications of employing intersectional principles in qualitative health research conducted in migration contexts, specifically focusing on a doctoral research project on return migration and reunited couples in Mexico. The article highlights the integration of social justice and community-based research perspectives within an intersectional lens. Five key areas are examined, including recognizing diversity and agency among women who stay behind, navigating intersectional identities, understanding positionality, and advocating for populations made vulnerable by inadequate policies, navigating power dynamics and multiple social locations, and empowering the community through intersectional research. The application of intersectionality challenges homogenizing narratives, emphasizing the agency and resilience of women who stay behind. Reflexivity is crucial in mitigating biases and deepening insights, while collaboration with a local researcher enhances understanding of power dynamics. By empowering the community through advisory committees and culturally relevant dissemination, I aimed to amplify community member voices and promote social justice. This article serves as a valuable resource for researchers conducting intersectional qualitative health research in rural settings, offering guidance on integrating a strength-based approach, fostering intersectional reciprocity, and navigating positionalities.