Multispecies fisheries pose a considerable management difficulty with respect to quota allocation between species. The distribution of total allowable catches (TACs) between species without considering fish community structure is altering the trophic interactions in the ecosystem and consequently impacts the natural productivity and the profitability of fishing. This paper aims to develop a methodological framework for assessing the composition and distribution of TACs within a heterogeneous fleet in a multispecies interaction system. The advantage of the presented approach combining a multispecies biological model with an economic model of individual vessel decisions is a possibility to analyze the harvest choice in the context of dynamic and changing conditions, where each action has a consequence for the future. An empirical application is provided for the Polish Baltic Sea fleet, where the most valuable target species is cod. The regulatory body sets the annual quota based on the target fishing mortality varying between scenarios. The net present value of the fishery in each scenario is compared by simulating stock changes over time and paired with stock collapse probability estimates.