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Bogotá, the capital city of Colombia, is mostly located on a lacustrine soil deposit surrounded by hills in a central plateau of the eastern cordillera of the Colombian Andes. This highly populated urban area is exposed to a significant seismic hazard from local and regional fault systems. In addition, the potential ground motion amplification during earthquakes due to the presence of soft soil deposits, along with the effects of the surface and subsurface topography, can strongly influence the seismic hazard and consequently the seismic risk to the city. This study aims to develop a physics‐based framework to generate synthetic ground records that can help better understand the seismic response of the basin and other amplification effects during strong earthquake shaking in the region, and to incorporate these effects into the estimation of seismic risk. To this end, a set of simulations were first conducted on Hercules, the wave propagation octree‐based finite element simulator developed by the Quake Group at Carnegie Mellon University, to identify the impacts of hypothetical strong earthquakes scenarios. Then, the results from these simulations were integrated with the exposure and vulnerability information previously developed for the main building constructions in the city to assess the seismic risk in the region under different conditions of analysis. Results from this more detailed model are compared with previously published results from simplified models. Sensitivity analyses help identify critical aspects that should be considered in the future to improve the seismic risk assessment of infrastructure. [ABSTRACT FROM AUTHOR]