Background Despite access to free antiretroviral therapy (ART) for all people living with human immunodeficiency virus (HIV), noncompliance to treatment continues to be a significant challenge in Eswatini. Yet studies investigating barriers to ART adherence in Eswatini are scarce. Most notably, there is a lack of research regarding rural women in Eswatini, who are currently the country's most vulnerable to HIV infection. Therefore, the objective of the study is to investigate individual, household, and community level barriers to ART adherence among rural women living with HIV. Methods We conducted a qualitative study to investigate individual, household, and community level barriers to ART adherence. We conducted focus group discussions with HIV-infected women (n = 4) from rural villages in Eswatini, and in-depth interviews with healthcare workers (n = 8) serving the area clinics. Open and axial coding techniques were used for data analysis and interpreted within a social ecological framework. Results Our findings revealed several individual level barriers including hunger, side effects of ART, personal stress, lack of disclosure of HIV status, alcohol use, and forgetting to take ART. Lack of food, unemployment and scarcity of financial resources were identified as critical barriers at the household level. Community and institutional barriers encompassed factors related to health delivery such as lack of privacy, travel time, transportation costs, excessive alcohol use by healthcare workers, maltreatment, public and self-stigma, gossip, and long waits at clinics.