© 2018 Ayieko et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background Despite substantial progress, gaps in the HIV care cascade remain large: globally, while about 36.7 million people were living with HIV in 2015, 11.9 million of these individuals did not know their HIV status, 12.7 million were in need of antiretroviral therapy (ART) and 13.0 million were not virally suppressed. We sought to deepen understanding of the barriers to care engagement at three critical steps of the care cascade proposed to make greatest impact for attaining the UNAIDS 90-90-90 targets aimed at shutting down the HIV epidemic. Methods Analyses were conducted among HIV-infected adults in rural East Africa. Qualitative data were collected using in-depth interviews among 63 individuals participating in an ongoing test-and treat trial (NCT01864683) in its baseline year (July 2013-June 2014). Audio recordings were transcribed, translated into English, and coded using Atlas.ti software. Data were analyzed using a thematic framework for explaining barriers to care engagement that drew upon both theory and prior empirical research in similar settings. Results Multiple barriers to engagement in care were observed. HIV-related stigma across dimensions of anticipated, internalized and enacted stigma manifested in denial and fears of disclosure, and influenced lapses in care engagement across multiple steps in the cascade. Poverty (lack of food and transport), lack of social support, work interference, prior negative experiences with health services, drug side effects, and treatment fatigue also negatively affected ART adherence and viral suppression. Gender differences were observed, with work interference and denial disproportionately affecting men compared to women. Conclusion Multiple barriers to HIV care engagement still pervade rural sub-Saharan settings threatening the realization of the UNAIDS 90-90-90 targets. To control the epidemic, efforts need to be accelerated to combat stigma. Patient economic empowerment, innovative drug formulations, as well as more patient-responsive health systems, may help overcome barriers to engagement in care.