Marine protected areas (MPAs) are increasingly proposed as a fisheries management tool besides their conservation purposes. When assessing the ecological, economic, and social-cultural impacts of protection, the dynamics of fisheries and fishers reallocation within and around multiple-use MPAs should be analyzed. Despite this, few studies incorporate the baseline information of fisheries distribution, therefore compromising an understanding of fishers’ preferences, choices and constrains before losing fishing grounds through the establishment of zoning and protection measures. To fulfil this gap, here we assess the spatial and seasonal fishers’ preferences from local artisanal fisheries (nets, traps, jigs and longlines) before the implementation of a MPA management plan (the Arrábida Marine Park, Portugal). Zero inflated modelling, hotspot analysis, vessels distribution range and site fidelity statistics showed that the main drivers of fishing effort allocation are the placement of preferred fishing grounds which are likely related to the distribution of target species and associated habitats. Proximity to port, weather conditions and distance to coast are also important factors influencing, in different ways, these artisanal fisheries. Our findings highlight the complex dynamics of the distribution of artisanal fisheries operating multiple-gears and targeting multiple-species and are likely transferable to many coastal multiple-use MPAs where no baseline data exist. Moreover, the variety of responses and preferences found between gears and fishers before the establishment of zoning are important to understand the dynamics of local fisheries, to contribute to an ecosystem-based management and to improve both conservation and fisheries management decisions. Our study is one of the few characterizing fisheries dynamics and fishers’ preferences before protection measures are implemented providing important lessons to the management of coastal fisheries where artisanal fisheries prevail.