© 2016 Brata et al.Background: Research has shown that the current practice of pharmacy staff when providing self-medication consultations in Indonesia is suboptimal. To improve the performance of pharmacy staff when providing self-medication consultations in community pharmacies, the factors that influence current practice need to be understood. The aim of this study is to identify the factors that influence current practice of pharmacy staff when handling self-medication consultations in Eastern Indonesian community pharmacies. Methods: Fifteen in-depth interviews were conducted with pharmacists, pharmacy technicians, pharmacy owners, and counter attendants. Thematic analysis was used to generate findings. Results: The current practice of pharmacy staff when handling self-medication consultations is directly influenced by the professionalism of pharmacy staff and patient responses to the consultations. These factors are in turn affected by the organisational context of the pharmacy and the external pharmacy environment. The organisational context of the pharmacy includes staffing, staff affordability, and the availability of time and facilities in which to provide consultations. The external pharmacy environment includes the number of trained pharmacy staff in the research setting, the relevance of pharmacy education to the needs of pharmacy practice, the support offered by the Indonesian Pharmacists Association, a competitive business environment, and the policy environment. Conclusion: Complex and inter-related factors influence the current practice of pharmacy staff when providing self-medication consultations in community pharmacies in this research setting. Multiple strategies will be required to improve consultation practices.