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Background: One of the main difficulties in consolidating malaria control programs lies in the incidence of asymptomatic infections in which people become reservoirs of the parasite without receiving treatment. In addition, military personnel represent a highly mobile population, promoting transmission hotspots of Plasmodium spp. from endemic to non-endemic areas. Methods: A cross-sectional study with stratified sampling (n = 806) was estimated in four departments (Antioquia, Chocó, Córdoba, and Nariño) with the highest malaria prevalence. Peripheral blood and thick smears, serological rapid diagnostic tests (RDT), a nested PCR, and a qPCR were used to identify asymptomatic malaria parasite carriers (AMPC). Additionally, patients were interviewed to determine their associated risk history. Results: Three out of 775 samples collected were positive by microscopy: two P. falciparum (El Bagre and Chocó) and one P. vivax (Carepa). Only one positive P. falciparum RDT was obtained in Chocó. Molecular diagnosis confirmed the presence of P. falciparum in the last sample according to the 18S marker (205 bp) and later verified by ssrRNA Sanger sequencing (1,200 bp). Consequently, the prevalence of asymptomatic malaria was estimated at 0.56% in Carepa, 1.92% in El Bagre, and 0.57% in Chocó. Conclusions: The prevalence of asymptomatic infections by Plasmodium spp. in the departments of Antioquia and Chocó did not exceed 2%. Previous malaria episodes, patrolling, or place of birth associated exposure were identified as risk antecedents in all positive cases. The implications of these results are discussed. [ABSTRACT FROM AUTHOR]