Long‐lived orogens are often characterized by basement blocks affected by polyphase thick‐skinned deformation. Deciphering these events is challenging due to the heterogeneous and complex structural histories resulting from the superposition of multiple deformation phases. For instance, the Central Cordillera of Colombia was shaped by multiple tectonic phases during the Mesozoic and Cenozoic, which have been poorly constrained in both space and time. To unravel the deformation history of this mountain belt, we conducted field mapping and applied a multi‐chronometric approach that included zircon and apatite U‐Pb dating of the igneous basement, epidote and titanite U‐Pb dating of structurally controlled mineralization events, K‐Ar dating of fault rock illite, and fission track and (U‐Th‐Sm)/He bedrock thermochronology of apatite and zircon. The results reveal six deformation events along two fault systems during the past 184 Myr. This deformation history started in the Jurassic with structurally controlled magmatism and ductile deformation; followed by brittle‐ductile and fluid‐assisted basin subsidence and inversion during the Cretaceous. Finally, the Cenozoic was characterized by brittle strike‐slip and compressional deformation. Our findings show the basement response to polyphase reworking, highlighting the prominent role of ancient upper‐plate discontinuities, magmatism, and fluids.