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 - PDs), using Pakistan as a case study. Our mixed-methods study synthesised insights from a survey of 419 systematically sampled PDs and 68 semi-structured interviews with PDs (n=28), pharmaceutical sales representatives (SRs) (n=12), and provincial and national policy actors (n=28). For the survey, we built a verified database of all registered PDs 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. Our survey showed that 90% of PDs met pharmaceutical SRs 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 an over-saturated pharmaceutical market. Regular interactions between pharmaceutical companies and PDs are normalised in our study setting. Progress on regulating these is hindered by the substantial role of incentive-linked prescribing in the financial success of physicians and 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 policy-makers concerned about curtailing growth of the pharmaceutical industry.