The northern section of the Danajon Bank, which is located in the Central Visayas islands of the Philippines is a shallow, tropical reef system that supports a multi-species fishery that is primarily artisanal and subsistence in nature. A persisting management and regulatory challenge in the area is the continued use of illegal fishing gears that are deemed destructive by either their manner of operation or technical design. In this study, we used a dynamic simulation model – Ecopath with Ecosim (EwE) – to explore the potential biological and socio-economic consequences of a hypothetical successful ban on the illegal fisheries in the area under two main scenarios: without fishing effort reallocation and with fishing effort reallocation. The highlight of the study relates to the profit-income analysis whereby the calculated increases in harvestable group biomasses did not necessarily translate into expected increases in overall yields and profits, but showed noteworthy impacts at the per capita level of specific fishing operations. The magnitude and direction of profit income changes varied for the two scenarios. All in all, the removal of illegal fisheries can be a “profitable” endeavor without necessarily having to sacrifice fisheries jobs through a reallocation of displaced illegal fishers to the legal fishery types. By doing so, the weighted average per capita net profit income in the Danajon municipal fisheries could be increased substantially (38%) compared to the present day reference level. To operationalize the fishing effort reallocation, we advocate the use of the fisheries licensing system that is already in place and to translate our findings into numbers of fishing license quantities to be allocated among the allowable fishery gear types. To conclude, the use of a per capita yield and profit incomes analysis provides relevant, objective, and practical policy advice for the management of small-scale and subsistence fisheries where alternative livelihood options may be limited.