BACKGROUND: Many countries implementing pro-poor reforms to expand subsidized health care, especially for the poor, recognize that high-quality healthcare, and not just access alone, is necessary to meet the Sustainable Development Goals. As the poor are more likely to use low quality health services, measures to improve access to health care need to emphasise quality as the cornerstone to achieving equity goals. Current methods to evaluate health systems financing equity fail to take into account measures of quality. This paper aims to provide a worked example of how to adapt a popular quantitative approach, Benefit Incidence Analysis (BIA), to incorporate a quality weighting into the computation of public subsidies for health care. METHODS: We used a dataset consisting of a sample of households surveyed in 10 provinces of Indonesia in early-2018. In parallel, a survey of public health facilities was conducted in the same geographical areas, and information about health facility infrastructure and basic equipment was collected. In each facility, an index of service readiness was computed as a measure of quality. Individuals who reported visiting a primary health care facility in the month before the interview were matched to their chosen facility. Standard BIA and an extended BIA that adjusts for service quality were conducted. RESULTS: Quality scores were relatively high across all facilities, with an average of 82%. Scores for basic equipment were highest, with an average score of 99% compared to essential medicines with an average score of 60%. Our findings from the quality-weighted BIA show that the distribution of subsidies for public primary health care facilities became less 'pro-poor' while private clinics became more 'pro-rich' after accounting for quality of care. Overall the distribution of subsidies became significantly pro-rich (CI = 0.037). CONCLUSIONS: Routine collection of quality indicators that can be linked to individuals is needed to enable a comprehensive understanding of individuals' pathways of care. From a policy perspective, accounting for quality of care in health financing assessment is crucial in a context where quality of care is a nationwide issue. In such a context, any health financing performance assessment is likely to be biased if quality is not accounted for.