Introduction <p>The present study aimed to evaluate the effect of motivational interviews and peer education on adherence to pre-exposure prophylaxis (PrEP) among key populations in Kisangani.</p> Methods <p>This study utilizes a randomized controlled trial design to assess the effect of motivational interviewing and peer education on adherence to PrEP among key populations in Kisangani, DRC. The trial was conducted over 12 months, with data collection points at baseline and each month. In total, 141 participants agreed to participate in the study, and after evaluating the eligibility criteria, 126 met the criteria and were randomly assigned to the two study groups. Intervention group: Participants received monthly adherence counseling on PrEP, and motivational interviews with healthcare providers at the friendly centers. Peer educators also sensitized them on PrEP adherence within their residential and social environments. Control group: Participants were monitored on PrEP according to routine procedures at the friendly centers. Participants were randomly assigned to either the intervention or control group based on their order of enrollment. Data were collected at the friendly centers for key populations at enrollment visits and, during follow-up visits. Survival analysis was performed using Kaplan-Meier survival curves, and survival curves were compared using the Log-Rank test. Hazard ratios (HR) derived from the Cox model and their confidence intervals were presented.</p> Result <p>We found that in the intervention group, 52 participants (82.5%) adhered to PrEP over the twelve months, compared to 16 participants (25.3%) in the control group (<i>p</i> &lt; 0.0001). Without intervention, the risk of non-adherence was five times higher in the control group (HR 4.9, 95%CI [1.6937–14.2823], <i>p</i> = 0.003). Factors that strengthened adherence to PrEP included attending appointments for ARV refills (HR 0.15, 95% CI [0.0720–0.3404], <i>p</i> &lt; 0.0001) and having adherence support (HR 0.26, 95% CI [0.1280–0.5482], <i>p</i> &lt; 0.0001).</p> Conclusion <p>Although the data confirm higher adherence in the intervention group, the high HIV incidence rate in the control group can be explained not only by the absence of the intervention but also by other factors related to the participants’ lives that may have contributed to the higher seroconversion rate compared to the intervention group.</p> Trial registration <p>PACTR202412535326702 registered in the Pan African clinical trials registry on December 2, 2024.</p>