The Philippine fisheries sector continues to play a critical role in the livelihood of coastal households; however, the country’s fisheries production level has been declining at the municipal level. To reverse this trend, marine protected areas are established in critical geographic areas to ensure that management and conservation follow sustainable fishing practices. Mabini, Davao de Oro, and San Isidro, Davao Oriental are coastal municipalities located in the southern Philippines. Mabini is a declared National Integrated Protected Area System (NIPAS) while San Isidro is a non-NIPAS fishing area. This paper aimed to identify the determinants of coastal fish catches among 406 fisherfolks in both Mabini and San Isidro during the Northeast Monsoon season during 2018–2019. The study utilized power analysis to calculate the sample size for two independent groups. Stratified random sampling was used to determine the respondents in each village. Further, quantile regression was used to estimate the Cobb–Douglas production function model in determining the impact of the drivers across varying fish catch levels. Effort time, boat length, input costs, other costs, distance, and boat type are significant drivers of catch output in Mabini, while for San Isidro, effort time, input costs, other costs, and distance variables are positively associated with fish output. Compared with San Isidro, fishers in Mabini using motorized boats have relatively higher fish catch levels, which is more pronounced in upper catch quantiles. Thus, access to motorized boats is crucial in addressing the impact of regulatory restrictions on fishers’ livelihood in marine protected areas.