The genus Cinchona L. has important medicinal, cultural, and economic value and is the emblematic tree of Peru. The genus is mainly found in the cloud forests of the Andes. However, the expansion of agriculture and livestock farming in the department of Amazonas is degrading these ecosystems and has reduced the size of the genus’s populations. In this work, we model the potential distribution under current conditions of three Cinchona species (C. capuli L. Anderson, C. macrocalyx Pav. Ex DC., and C. pubescens Vahl.) to identify areas with a high likelihood of species presence and their key conservation and reforestation zones. We fitted a maximum entropy (MaxEnt) model using nineteen bioclimatic variables, three topographic variables, nine edaphic variables, and solar radiation. Under current conditions, the potential distribution of C. capuli covers 17.22% (7243.98 km2); C. macrocalyx, 29.11% (12,238.91 km2); and C. pubescens, 22.94% (9647.63 km2) of the study area, which was mostly located in central and southern Amazonas. Only 24.29% (25.51% of C. capuli, 21.02% of C. macrocalyx, and 26.35% of C. pubescens) of the potential distributions are within protected areas, while 10,987.22 km2 of the surface area of the department of Amazonas is degraded, of which 29.80% covers the area of probable occurrence of C. capuli, 38.72% of C. macrocalyx, and 34.82% of C. pubescens. Consequently, it is necessary to promote additional conservation strategies for Cinchona, including the establishment of new protected areas and the recovery of degraded habitats, in order to protect this species.