Objective This study aimed to evaluate the seroprevalence of anti-SARS-CoV-2 IgG and factors associated with the infection among PLWHIV over the first 12 months following the outbreak of COVID-19 in Burkina Faso. Design A retrospective cross-sectional study of plasma samples collected from March 9, 2020, and March 8, 2021, at the outpatient HIV referral center, before the introduction of the SARS-CoV-2 vaccine in Burkina Faso. Methods Anti-SARS-CoV-2 IgG were detected in plasma using DS-ЕIA-ANTI-SARS-CoV-2-G (S) kit. Logistic regressions were used to compare SARS-CoV-2 specific immune responses between groups and within subgroups. Results and discussion A total of 419 plasma were subjected to serological diagnosis. None of the participants was vaccinated against COVID-19 during the period of sample collection, and 130 samples were positive for anti-SARS-CoV-2 IgG, giving a prevalence of 31.0% (95% CI 26.6–35.7). The median CD4 cell count was 661 cells/μL (IQR,422–928). Retailers had half the risk of being infected compared to housemaids with an OR of 0.49 ( p = 0.028, 95% CI 0.26–0.91). Likewise, the risk of infection was 1.69 times higher in patients on integrase inhibitors compared to that of patients on non-nucleoside reverse transcriptase inhibitors ( p = 0.020, 95% CI 1.09–2.63). Conclusion Our study reveals a high seroprevalence among PLWHIV to SARS-CoV-2 during the first year of the pandemic. In addition, PLWHIV on integrase inhibitors are 1.69 times more likely to be infected than PLWHIV on non-nucleoside inhibitors, and this observation remains an intriguing topic that still needs to be clarified.