BACKGROUND: The UK Quality and Outcomes Framework (QOF) offers financial incentives to deliver high-quality care for individual diseases, but the single-disease focus takes no account of multimorbidity.AIM: To examine variation in QOF payments for two indicators incentivised in ≥1 disease domain.DESIGN AND SETTING: Modelling study using cross-sectional data from 314 general practices in Scotland.METHOD: Maximum payments that practices could receive under existing financial incentives were calculated for blood pressure (BP) control and influenza immunisation according to the number of coexisting clinical conditions. Payments were recalculated assuming a single new indicator.RESULTS: Payment varied by condition (£4.71-£11.08 for one BP control and £2.09-£5.78 for one influenza immunisation). Practices earned more for delivering the same action in patients with multimorbidity: in patients with 2, 3, and ≥4 conditions mean payments were £13.95, £21.92, and £29.72 for BP control, and £7.48, £11.21, and £15.14 for influenza immunisation, respectively. Practices in deprived areas had more multiple incentivised patients. When recalculated so that each incentivised action was only paid for once, all practices received less for BP control: affluent practices received more and deprived practices received less for influenza immunisation.CONCLUSION: For patients with single conditions, existing QOF payment methods have more than twofold variation in payment for delivering the same process. Multiple payments were common in patients with multimorbidity. A payment method is required that ensures fairness of rewards while maintaining adequate funding for practices based on actual workload.