The Eastern Cordillera of Colombia rose to maximum elevations of >5 km during the Cenozoic by inversion of a Mesozoic rift basin. Previous studies proposed that the exhumation of the Eastern Cordillera increased from ~6 Ma to the present due to the interplay between tectonic shortening and climate. In this study, we integrate new field observations, structural data, low‐temperature thermochronology, thermobarometry, and vitrinite reflectance along a section through the Tablazo, Cocuy, and Llanos regions to estimate the amount of shortening and the exhumation history. Our results indicate that shortening started as early as the latest Maastrichtian‐Paleocene in the Tablazo and Cocuy regions. Exhumation migrated eastward, starting in the Paleocene in the west and continuing in the Miocene in the east. The amount and rate of exhumation peaked in the Cocuy region with values of <5 km and < 0.4 km/Ma, respectively. At the highest elevations in the Cocuy Sierra, we also found evidence of a low‐pressure/high‐temperature metamorphic overprint, possibly related to shallow and local magmatic intrusions that occurred in the Late Miocene. Our cross‐section interpretation suggests a low amount of shortening (13%) that is mainly accommodated by high‐angle inverted faults and by the frontal thrust system. The presence of shallow magmatic bodies, moderate exhumation, and low shortening raises questions about the processes (isostatic versus dynamic) that drove the topographic growth of the high Cocuy Sierra.