How to strengthen local capacity through donor-funded projects remains opaque. Using the European Centre for Development Policy Management's core capabilities model to examine a project engaging local organisations, we identify capabilities differentiating performance and gains from project participation. The studied organisations were often weak in capabilities important for successfully working with local governments. Some strengthened capacity, but improvements were concentrated in capabilities related to complying with donors’ requirements rather than capabilities enhancing performance. We question assumptions underlying programme designs based on Organisation for Economic Co-operation and Development's donor-country cooperation principles, and offer suggestions for balancing capacity gains to sustain independent local organisations.