Background In May 2009, the Northern Ireland government introduced General Dental Services (GDS) contracts based on capitation in dental practices newly set up by a corporate dental provider to promote access to dental care in populations that had previously struggled to secure service provision. Dental service provision forms an important component of general health services for the population, but the implications of health system financing on care delivered and the financial cost of services has received relatively little attention in the research literature. The aim of this study is to evaluate the policy effect capitation payment in recently started corporate practices had on the delivery of primary oral healthcare in Northern Ireland and access to services. Methods We analysed the policy initiative in Northern Ireland as a natural experiment to find the impact on healthcare delivery of the newly set up corporate practices that use a prospective capitation system to remunerate primary care dentists. Data was collected from GDS claim forms submitted to the Business Services Organisation (BSO) between April 2011 and October 2014. Health and Social Care Board (HSCB) practices operating within a capitation system were matched to a control group, who were remunerated using a retrospective fee-for-service system. Results No evidence of patient selection was found in the HSCB practices set up by a corporate provider and operated under capitation. However, patients were less likely to visit the dentist and received less treatment when they did attend, compared to those belonging to the control group (P < 0.05). The extent of preventive activity offered and the patient payment charge revenue did not differ between the two practice groups. Conclusion Although remunerating NHS primary care dentists in newly set up corporate practices using a prospective capitation system managed costs within healthcare, there is evidence that this policy may have reduced access to care of registered patients. Electronic supplementary material The online version of this article (doi:10.1186/s12913-017-2117-3) contains supplementary material, which is available to authorized users.