Background Cambodia targets P. falciparum malaria elimination by 2023 and all human malaria species by 2025, aligning with WHO’s Mekong Malaria Elimination program. The Intermittent Preventive Treatment for Forest Goers (IPTf) project aimed at forest-specific malaria elimination. The study aims to pinpoint the main factors driving malaria transmission in Cambodian forests and evaluate the initial implementation and effectiveness of IPTf in accelerating the elimination of malaria by treating and preventing infections among at-risk populations in these areas. Methods From March 11, 2019, to January 30, 2021, a malaria intervention program took place in isolated forests in Northeast Cambodia. The first phase focused on observing forest goers (FGs) within the forests, documenting their malaria risk. In the second phase, a monthly artesunate-mefloquine IPTf was implemented by trained forest malaria workers who were former FGs conducting interviews, blood collection, and IPTf administration. Findings Throughout the two-year period, 2198 FGs were involved in 3579 interviews, with 284 in both the observation and intervention phases. Following IPTf implementation, PCR-confirmed malaria prevalence significantly decreased from 2.9% to 0.5% for P. falciparum and from 21.0% to 4.7% for P. vivax. Among the 284 participants tracked through both phases, malaria prevalence fell from 2.5% to 0.3% for P. falciparum and from 22.5% to 3.7% for P. vivax. The intervention phase demonstrated a rapid decline in P. falciparum prevalence among mobile and previously inaccessible populations, while also revealing a higher P. falciparum infection risk associated with activities inaccurately labelled as farming, underscoring the need for customized interventions. Interpretation The successful implementation of IPTf in Cambodia’s remote forests has markedly decreased malaria prevalence among high-risk groups. Cambodia’s National Malaria Program has acknowledged this strategy as essential for malaria elimination intervention, endorsing forest-specific approaches to meet the 2025 goal of eradicating all human malaria species in Cambodia.