Large, long-lived marine animals (‘marine megafauna’) play critical roles in ocean ecosystems, however, they are threatened by overfishing. Technologies and practices that reduce fisheries’ impacts on marine megafauna are well documented, yet less is known about how to encourage their adoption. This is particularly challenging in small-scale fisheries (SSFs), where endangered species can have important consumptive use values. We used a novel combination of methods – scenario interviews with contingent valuation (CV) – to investigate how incentive-based interventions might influence fisher behaviour and reduce mortality of Critically Endangered taxa (hammerhead sharks (Sphyrna spp.) and wedgefish (Rhynchobatus spp.)) in two case study SSFs in Indonesia. Scenario interviews revealed that positive performance-based incentives were almost unanimously supported (98% and 96% of fishers would stop landing hammerheads and wedgefish, respectively). This is in contrast to 1% and 6% under a business as usual control scenario, and 52% and 46% in response to a regulation with a fine. Using CV, we estimated that an incentive-based scheme for catch mitigation of all hammerheads and wedgefish across both sites could cost US$71,620-298,820 annually, and save up to 18,500 hammerheads and 2,140 wedgefish relative to current catch baselines. This study provides empirical evidence that performance-based payments could offer a cost-effective, legitimate and socially-just approach for marine conservation in SSFs, and support “a sustainable and equitable blue economy” and “living in harmony with nature”. This is particularly important with the growing adoption of net-outcome goals for biodiversity, with studies such as this providing the basis for locally-appropriate investment ready schemes for bycatch-neutral seafood supply chains.