Achieving target reference points for multiple species within a fishery, rather than managing by a single key species, can present challenges for fisheries management. A multi-species fishery is where fishers or operations can retain many species from deploying their fishing gear and effort and are common in Queensland. The east coast otter trawl fishery (ECOTF) is a large effort managed multi-species fishery in Queensland, catching up to 6000 tonnes of product from a diverse array of species. This research investigated how to combine multiple species, with and without stock assessments, into a single regional-specific trawl effort cap, for two regions of the ECOTF. Key aspects of the methods included two calculation methods differing in their complexity (detailed or ratio), two different inshore and offshore spatial stratifications (filtered or allocated divisions within a region), two different co-caught adjustments (species importance based on effort or catch data) and different species inclusions. These comparisons resulted in 64 different effort cap calculations per region. Findings highlighted important regional differences mainly driven by the number of targeted and retained species and their order of importance among species to commercial operators. Adding additional species to calculations had little impact.