Background Internalization of HIV-related stigma may inhibit a person’s ability to manage HIV disease through adherence to treatment regimens. Studies, mainly with white men, have suggested an association between internalized stigma and sub-optimal adherence to antiretroviral therapy (ART). However, there is a scarcity of research with women of different racial/ethnic backgrounds and on mediating mechanisms in the association between internalized stigma and ART adherence. Methods The Women’s Interagency HIV Study (WIHS) is a multi-center cohort study. Women living with HIV complete interviewer-administered questionnaires semi-annually. Cross-sectional analyses for the current article included 1168 women on ART for whom data on medication adherence were available from their last study visit between April 2013 and March 2014, when the internalized stigma measure was initially introduced. Results The association between internalized stigma and self-reported sub-optimal ART adherence was significant for those in racial/ethnic minority groups (AOR = 0.69, p = .009, CI [0.52, 0.91]), but not for non-Hispanic whites (AOR = 2.15, p = .19, CI [0.69, 6.73]). Depressive symptoms, loneliness, and low perceived social support mediated the association between internalized stigma and sub-optimal adherence in the whole sample, as well as in the subsample of minority participants. In serial mediation models, internalized stigma predicted less perceived social support (or higher loneliness), which in turn predicted more depressive symptoms, which in turn predicted sub-optimal medication adherence. Conclusions Findings suggest that interconnected psychosocial mechanisms affect ART adherence, and that improvements in adherence may require multi-faceted interventions addressing both mental health and interpersonal factors, especially for minority women.