Female sex workers (FSW) and men who have sex with men (MSM) are disproportionately affected by HIV. Oral pre-exposure prophylaxis (PrEP) has become increasingly available in African countries including the Democratic Republic of Congo (DRC). However, limited data exist on PrEP uptake and retention or on factors that affect PrEP use among FSW and MSM. This mixed-method study, conducted at KP-friendly centers in Kinshasa, DRC, aimed to identify patterns of PrEP retention and to understand underlying factors of PrEP engagement. Collected data included programmatic data, extraction of routine clinical records, and qualitative interviews with FSW and MSM. Logistic regression was used to identify factors associated with PrEP retention. Qualitative data were analyzed thematically. Findings were then synthesized. Low rates of PrEP initiation and retention were of concern. Only 25% of eligible FSW and MSM initiated PrEP in 2019-2022. Among FSW, 79% returned to the clinic for PrEP refills at 1 month, with only 15% returning for a 3-month visit. Similarly, 74% of MSM were retained at 1 month, with 10% retained at 3 months. Previous experience using PrEP was significantly associated with retention at 3 months. Qualitative analyses identified stigma, side effects, dislike of daily medication regimen, and a shortage of KP-friendly facilities as major barriers to PrEP engagement. This warrants the need for interventions to strengthen messaging about PrEP and side effects wading over time. Raising awareness among the Congolese general population may help to avoid stigmatization of PrEP users and improve PrEP acceptance among key populations at risk.