The Philippines is working to eliminate malaria by 2030 using a subnational approach, with strategies tailored to the endemicity of the province. Eliminating malaria in the remaining 7 provinces still reporting cases requires improved and innovative surveillance with more sensitive, reliable and practical tools that are capable of detecting both past and present, including asymptomatic, sub-patent infections. This work reports the results of a multiplex serological assay (Luminex) specific to P. falciparum and P. vivax performed on dried blood spot samples collected in health facility surveys, carried out in 3 sites with varying malaria burden from June 2016 to January 2018. A total of 4,105 samples from Palawan, 1501 from Occidental Mindoro and 559 from Bataan were tested to determine (a) individual antibody response to malaria-specific antigens, (b) the proportion of seropositive individuals in different age groups, and (c) recent and cumulative exposure. Cut-off values for seropositivity were calculated individually for each species and antigen using a mixture model previously described. Age-specific seroprevalence of antibodies were fitted into reversible catalytic models using maximum likelihood methods to derive seroconversion rates of the population. Comparison of AMA-1 seroprevalence for children (0-4 years old) and adults (25 years old and above) between the 3 sites show >20% and >80% respectively for Palawan, against <6% and <50% for both Occidental Mindoro and Bataan, indicating continuous and intense malaria transmission in Palawan, and minimal, or probably nil, transmission in the 2 other sites. Combining serology and geospatial data showed distinct spatial patterns of local transmission in the 3 sites, underlining potential areas for targeted elimination activities. The implications of these findings on the current surveillance system and the prospect of integrating serological and geospatial markers, along with other measures, to improve surveillance for better targeting of malaria elimination in the Philippines will be discussed.