Over the past decade, efforts have been made to factor technical interactions into management recommendations for mixed fisheries. Yet, the dynamics underlying joint production in mixed fisheries are generally poorly captured in operational mixed fisheries models supporting total allowable catch advice. Using an integrated ecological–economic simulation model, we explore the extent to which fishers are likely to alter the species composition of their landings in a mixed fishery managed with individual transferable quotas, the Australian Southern and Eastern Scalefish and Shark Fishery. Our simulations capture three different types of joint production problems, highlighting the flexibility that exists in terms of achievable catch compositions when quota markets provide the economic incentives to adapt fishing practices to quota availability. These results highlight the importance of capturing the drivers of fishing choices when advising TAC decisions in mixed fisheries. We also identify a hierarchy of species in this fishery, with harvest targets set for primary commercial species determining most of its socio-economic performance.