The petroleum potential of onshore basins in Colombia has been partly controlled by the Andean Orogeny since the end of the Cretaceous. Its Axial Zone has at least one understudied active petroleum system with a rather low petroleum potential and few commercial medium to heavy oil accumulations, raising questions about how the Andean deformation influenced the petroleum system and the possible undiscovered accumulations. We examine the timing of this petroleum system in the Axial Zone through oil–source correlations and two 2D petroleum system models across the Boyacá and Soápaga faults based on cross-sections. Modelling reveals the direct control of deformation on generation–accumulation in the Axial Zone, where the Lower Cretaceous source rocks, due to high heat flows during the synrift phase, started generation so early (100 to 60 Ma) that no reservoirs or traps were yet available to allow hydrocarbon entrapment and accumulation. Equally, for the younger Upper Cretaceous source rocks, the tectonic inversion of the basin between 33 and 23 Ma along the Boyacá and Soápaga faults interrupted burial and the maturation in most parts of the basin, leaving only local pods of active source rocks where maturation continues today due to the tectonic overburden along the footwall of the Soápaga Fault. The latter is thus the major kitchen, contributing more than 50% of the liquid hydrocarbons trapped mainly in Upper Cretaceous and Paleocene sandstones. Hydrocarbons migrate upwards where biodegradation and water washing occurred in the near-surface, giving rise to the many tar sand occurrences in the Eocene sandstones.