Internationally, HIV-related stigma and crystal methamphetamine (meth) use have been described as barriers to treatment adherence among gay, bisexual, and other men who have sex with men (gbMSM). Crystal meth use has been increasing among gbMSM in the Metropolitan Area of Mexico City (MAMC). Therefore, this study aimed to determine the association between HIV-related stigma and HIV treatment adherence among gbMSM who use crystal meth in the MAMC. This study was undertaken as part of an exploratory study of crystal meth use in the MAMC. The data were collected from September to December 2021 through an encrypted online survey. Participants (n = 89) were gbMSM adults living with HIV who reported crystal meth use in the past month that were recruited through an online snowball sampling. The online survey included questions about HIV treatment adherence, sexual behaviors, the Alcohol, Smoking, and Substance Involved Screening Test, and the HIV-Related Stigma Mechanisms Scale. Logistic regression analyses assessed the association between HIV-related stigma and HIV treatment adherence. The multivariate logistic regression model showed that, controlling for health insurance [adjusted odds ratio (AOR) = 0.13; 95% confidence intervals (CI) = 0.02–0.59] and educational level (AOR = 0.16; 95% CI = 0.02–0.88), non-adherence to HIV treatment was independently associated with higher HIV-related stigma (AOR = 1.06; 95% CI = 1.01–1.12). Public health policies must include HIV-related stigma and substance use in treating gbMSM with HIV.