The institutional change induced by payments for ecosystem services (PES) schemes is a ‘messy’ process. The uptake and outcomes of PES schemes cannot be fully explained from a rational choice perspective. The notion of ‘institutional bricolage’ is needed to analyse how actors assemble or reshape their actions by combining new institutions such as a PES scheme within other locally embedded institutions. A case study from Japan is used to illustrate how a PES scheme designed to conserve the habitat of a charismatic and endangered flagship species, the Oriental White Stork, has been reshaped by social actors to fit the locally dominant ‘institutional logic’. We also show how the resulting institutional change is not only able to subvert policy makers’ original assumptions, for instance about how to target and distribute the payments, but can also contribute to the reproduction of unequal power relations.