Methods Primary care organizations (PCOs) in England are required to run a prescribing incentive scheme. The average payment received by general practitioners (GPs) under these schemes is not known. We conducted a longitudinal (2 year) questionnaire study of all PCOs in London and the south east of England aiming to explore the relationship between the financial incentives, the selection of prescribing indicators and success at remaining within budget. In the second year, the average reward per GP amounted to £1220 (range £470–£4330). Underspent PCOs made larger incentive scheme payments to their practices as did PCOs that had successfully overturned a first year overspend into a second year underspend. The size of rewards was unrelated to the selection of any particular cost‐ or quality‐based prescribing indicator. We conclude that larger prescribing incentive scheme payments may have contributed to prescribing cost control but their effect on prescribing quality is uncertain.