The northwesternmost portion of the Amazonian Craton outcrops in Eastern Colombia consists predominantly of Proterozoic tectonometamorphic provinces whose rocks range in age from 1.85 to 0.6 Ga. The assembly of the NW Amazonian Craton entails a complex and extensive geological history comprising most of the Proterozoic era, which is mostly poorly understood because of the lack of well-defined temporal and stratigraphic constraints. In this work, we present new zircon and apatite U-Pb data from two samples from the medium-to-high-grade rocks of the Guaviare Complex. From zircon U-Pb ages, the protolith age of the Guaviare Complex has been constrained at ca 1.3 Ga. However, in the present database as well as in our newly produced data, the conspicuous presence of a significant population of discordant ages was revisited showing zircon U-Pb ages that might indicate a reheating event between 1.0 to 0.6 Ga. Apatite U-Pb data from the same samples reinforces this interpretation by revealing consistent ages ca. 0.6 Ga. We interpret that the Late-Neoproterozoic-Ediacaran apatite U-Pb ages might be resulting from the thermal overprint caused by the large intrusions of Ediacaran nepheline syenite bodies in the Amazonian Craton, inducing local thermal metamorphism. This metamorphism generated granoblastic textures in the Guaviare Complex, resulting in the formation of granofels, quartzites and hornfels. On the other hand, zircon crystal grains also indicate recrystallization rims and some concordant data as result of an older tectonometamorphic event, likely related to the Putumayo Orogeny ca. 1.0 Ga, which initially would have affected the Guaviare Complex rocks and imprinted their predominating banding and foliation. We therefore unravel the metamorphic history of the Guaviare Complex and show how the application of distinct geochronometer is essential to decipher multiple metamorphic overprints in complex cratonic realms.