Abstract Following substantial progress in malaria control in the Philippines, new surveillance approaches are needed to identify and target residual malaria transmission. This study evaluated an enhanced surveillance approach using rolling cross-sectional surveys of all health facility attendees augmented with molecular diagnostics and geolocation. Facility surveys were carried out in 3 sites representing different transmission intensities: Morong, Bataan (pre-elimination), Abra de Ilog, Occidental Mindoro (stable-medium risk) and Rizal, Palawan (high risk, control). Only 1 RDT positive infection and no PCR confirmed infections were found in Bataan and Occidental Mindoro suggesting the absence of transmission. In Rizal, inclusion of all health facility attendees, regardless of symptoms, and use of molecular diagnostics identified an additional 313 infected individuals in addition to 300 cases identified by routine screening of febrile patients with RDT or microscopy. Of these, the majority (313/613) were subpatent infections and only detected using molecular methods. Simultaneous collection of GPS coordinates on tablet-based applications allowed real-time mapping of malaria infections. Risk factor analysis showed higher risks in children and indigenous groups, with bednet use having a protective effect. Subpatent infections were more common in men and older age groups. Overall, malaria risks were not associated with patient status and some of non-patient clinic attendees reported febrile illnesses (1.9%, 26/1369) despite not seeking treatment highlighting the widespread distribution of infection in communities. Together, these data illustrate the utility of health-facility based surveys to augment surveillance data to increase the probability of detecting infections in the wider community.