BACKGROUND: Despite advancement in Prevention of Mother to Child Transmission (PMTCT) services, the rate of MTCT of HIV in sub-Saharan Africa is still high. This is partly due to low retention of HIV positive mothers in HIV care. We sought to determine the level of retention and the factors associated with retention among HIV positive pregnant and breastfeeding mothers following accreditation of an antiretroviral therapy (ART) clinic to offer full time ART services in one of the lower health facilities in rural Western Uganda. METHODS: This study was a mixed methods study conducted in 5 health centres in rural Western Uganda from 10th April to 10th May 2017. A total of 132 retained and non-retained HIV positive pregnant and breastfeeding mothers were recruited. A Mother was categorized as retained if she had not missed her ART appointments at antenatal or postnatal clinic for ≥3 consecutive months. Questionnaires were administered and four focus group discussions were held. We used descriptive statistics to understand characteristics of mothers and their levels of retention. Thematic analysis was used to analyze qualitative data. RESULTS: About a third (35.6%) of the mothers were aged 18-24 with a median age of 26 (IQR 23, minimum age of 16 and maximum age of 39). More than half, 73 (55.3%) of all mothers were in HIV care for 3-24 months and about 116(87.9%) of all mothers were retained in HIV care. This was an improvement from 53% reported in 2015. We found lack of formal education, lack of disclosure of HIV status to the spouse, perceived lack of confidentiality and self stigmatization as factors hindering retention. The desire to have an HIV free baby, fear of death and opportunistic infections, support from significant others and community groups were factors associated with retention. CONCLUSIONS: We observed improved retention in lower health centres and to achieve 100% retention, we recommend interventions such as sensitizing HIV positive mothers on disclosure of HIV status to spouse, maintaining confidentiality of client information at the clinic, support to girl child education and formation of community support groups. TRIAL REGISTRATION: This study was retrospectively registered with the Uganda National Council for Science and Technology (UNCST), registration receipt number 10961 on the 9th March, 2018.