BACKGROUND: Despite known adverse impacts on patients and health systems, 'incentive-linked prescribing', which describes the prescribing of medicines that result in personal benefits for the prescriber, remains a widespread and hidden impediment to quality of healthcare. We investigated factors perpetuating incentive-linked prescribing among primary care physicians in for-profit practices (referred to as private doctors), using Pakistan as a case study. METHODS: Our mixed-methods study synthesised insights from a survey of 419 systematically samples private doctors and 68 semi-structured interviews with private doctors (n=28), pharmaceutical sales representatives (n=12), and provincial and national policy actors (n=28). For the survey, we built a verified database of all registered private doctors within Karachi, Pakistan's most populous city, administered an electronic questionnaire in-person and descriptively analysed the data. Semi-structured interviews incorporated a vignette-based exercise and data was analysed using an interpretive approach. RESULTS: Our survey showed that 90% of private doctors met pharmaceutical sales representatives weekly. Three interlinked factors perpetuating incentive-linked prescribing we identified were: gaps in understanding of conflicts of interest and loss of values among doctors; financial pressures on doctors operating in a (largely) privately financed health-system, exacerbated by competition with unqualified healthcare providers; and aggressive incentivisation by pharmaceutical companies, linked to low political will to regulate and an over-saturated pharmaceutical market. CONCLUSION: Regular interactions between pharmaceutical companies and private doctors are normalised in our study setting, and progress on regulating these is hindered by the substantial role of incentive-linked prescribing in the financial success of physicians and the pharmaceutical industry employees. A first step towards addressing the entrenchment of incentive-linked prescribing may be to reduce opposition to restrictions on incentivisation of physicians from stakeholders within the pharmaceutical industry, physicians themselves, and policymakers concerned about curtailing growth of the pharmaceutical industry.