Coral reefs offer valuable ecosystem goods and services, such as coastal protection, erosion regulation, fishery, biodiversity, habitat and nursery grounds. However, they face threats from anthropogenic activities, including poor water quality, global warming, coastal development and unsustainable fisheries. Marine Protected Areas (MPAs) provide a structured and holistic approach in addressing these threats. Regular monitoring and assessment of these MPAs are crucial components in evaluating the MPAs design and effectiveness. Two coral reefs (i.e. Poblacion and Kadurong Reefs) were established as MPAs in Liloan, Cebu, Philippines to protect crucial habitat and biodiversity with the hope of improving fisheries by avoiding fish stock disintegration. These coral reefs provide shelter to many commercially-significant fish species, supporting subsistence and livelihood in the community. These MPAs are not only biologically rich, but they also support socio-economic stability. Hence, management and protection of the coral reefs in the MPAs of Liloan, Cebu is of paramount importance. To formulate conservation and applicable management measures, research and monitoring should be in place. This paper presents the data collected from the short term monitoring in the Poblaction and Kadurong Reefs. The paper describes an important set of data that can be used by the stakeholders to benchmark biophysical assessments for management of marine-protected areas in Liloan. This data paper provides baseline information on the health of the coral reefs of the MPAs in Liloan, Cebu. Datasets covering physico-chemical and biological parameters inclusive of water quality, coral reef cover, fish and plankton occurrence and abundance were determined using the standard protocols for surveying tropical marine resources. The results will serve as a benchmark in formulating guidelines and implementing relevant policies for the effective management and protection of the MPAs in Liloan, Cebu, Philippines.