Like many other tropical countries, the Philippines has suffered from decades of deforestation and forest degradation during and even after the logging era. Several open access Earth Observation (EO) products are increasingly being used for deforestation analysis in support of national and international initiatives and policymaking on forest conservation and management. Using a combination of annual forest loss and near-real time forest disturbance products, we provide a comprehensive analysis of the deforestation events in three forest frontiers of the Philippines. A space-time pattern mining approach was used to map quarterly deforestation hotspots at 1 km pixel size (100 hectares), where hotspots are classified according to the spatial and temporal variability of the 2000–2020 deforestation in the study area. Our results revealed that 79–81% of the hotspots overlap with primary forests and 27–29% are inside the state-declared protected areas. The intra-annual analysis of deforestation in 2020 revealed an alarming trend, where most deforestation occurred between the 1st and 2nd quarter (92–94% in hotspot forests; 87–89% in non-hotspot forests), highly overlapping within the slash-and-burn farming season. We also found “new” hotspots (2020) formed mostly from landslide scars and partly from selective logging, the latter is believed to be underestimated. Our study paves the way for rapid and regular assessment of the country’s deforestation, useful for the respective environmental institutions who convene several times a year. Moreover, our findings assert the imperative of alternative livelihoods to upland farmers, efficient forest protection activities, and even the mitigation of landslide risks.