AbstractTropical deforestation varies temporally and spatially which can inhibit the ability of existing protected areas to stem forest loss. Identifying the spatial–temporal distribution of deforestation and its concentration can help decision makers decide conservation priorities and leverage limited resources. This study assessed how topographic and anthropogenic variables affect deforestation patterns within and outside protected areas on the islands of Sumatra and Kalimantan in Indonesia. Emerging hotspot analysis (EHA) was used to evaluate spatial and temporal trends of forest loss on the Hansen annual forest loss data for these islands from 2001–2018. For the two islands, most hotspots were detected outside protected areas; those within protected areas were mainly concentrated at boundaries, where lower elevation/slope and high human pressure could be observed. New hotspots were identified within the three PAs in Sumatra, while three kinds of hotspots (consecutive, oscillating, and sporadic) were found in the two PAs of Kalimantan (Kutai and Teluk Kelumpang). Areas with high human pressure (average human footprint higher than 12) were covered by a high density of hotspots. The results identify specific areas where forest loss has emerged recently, which could indicate a conservation priority. It is suggested that new protected areas be established in locations showing intensifying and persistent hotspots—those where deforestation has occurred for ≥16 of 18 years of the study period.