To improve access to health care services, an intervention was implemented in Burkina Faso granting full exemption from user fees. Two further components, staff training and supervision, were added to support the intervention. Our aim in this study was to examine how this tripartite intervention affected the quality of drug prescriptions. Using a mixed methodology, we first conducted an interrupted time series over 24 months. Nine health centres were studied that had previously undergone a process analysis. A total of 14 956 prescriptions for children 0-4 years old were selected by interval sampling from the visit registries from 1 year before to 1 year after the intervention's launch. We then interviewed 14 prescribers. We used three World Health Organization (WHO) indicators to assess drug prescription quality. Analysis was carried out using linear regression and logistic regression. The prescribers' statements underwent content analysis, to understand their perceptions and changes in their practice since the subsidy's introduction. One effect of the intervention was a reduced use of injections (odd ratio (OR) = 0.28 [0.17; 0.46]) in cases of acute lower respiratory tract infections (ALRTI) without comorbidity. Another was a reduction in the inappropriate use of antibiotics in malaria without comorbidity (OR = 0.48 [0.33; 0.70]). The average number of drugs prescribed also decreased (coefficient = -0.14 [-0.20; -0.08]) in cases of ALRTI without comorbidity. The prescribers reported that their practices were either maintained or improved. The user fees exemption programme, combined with health staff training and supervision, did not lead to any deterioration in the quality of drug prescriptions.