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In many African countries, user fees have failed to achieve intended access and quality of care improvements. Subsequent user fee reduction or elimination policies have often been poorly planned, without alternative sources of income for facilities. We describe early implementation of an innovative national health financing intervention in Kenya; the health sector services fund (HSSF). In HSSF, central funds are credited directly into a facility’s bank account quarterly, and facility funds are managed by health facility management committees (HFMCs) including community representatives. HSSF is therefore a finance mechanism with potential to increase access to funds for peripheral facilities, support user fee reduction and improve equity in access. We conducted a process evaluation of HSSF implementation based on a theory of change underpinning the intervention. Methods included interviews at national, district and facility levels, facility record reviews, a structured exit survey and a document review. We found impressive achievements: HSSF funds were reaching facilities; funds were being overseen and used in a way that strengthened transparency and community involvement; and health workers’ motivation and patient satisfaction improved. Challenges or unintended outcomes included: complex and centralized accounting requirements undermining efficiency; interactions between HSSF and user fees leading to difficulties in accessing crucial user fee funds; and some relationship problems between key players. Although user fees charged had not increased, national reduction policies were still not being adhered to. Finance mechanisms can have a strong positive impact on peripheral facilities, and HFMCs can play a valuable role in managing facilities. Although fiduciary oversight is essential, mechanisms should allow for local decision-making and ensure that unmanageable paperwork is avoided. There are also limits to what can be achieved with relatively small funds in contexts of enormous need. Process evaluations tracking (un)intended consequences of interventions can contribute to regional financing and decentralization debates.