Pubenza is a remarkable palaeontological site of Colombia, and a place that could hold some of the potentially oldest evidence of humans in northern South America. Previous palaeontological research at this site has mainly focused on the megafauna. Here we describe and establish the systematic palaeontology for the small fauna that inhabited this ancient lacustrine ecosystem, including the first report of birds, tortoises and vipers for the Late Pleistocene in Colombia. Furthermore, exceptionally well preserved fossilised wasp nests are morphologically and elementally characterised, which is the first report of an ichnofossil of this kind in northern South America. In addition, new material of kinosternid turtles, armadillos and rodents is also described. Our results reveal that the Bogotá River Basin, where Pubenza is located, was a rich ecosystem during the Late Pleistocene and a region of great interest for future articulated palaeontological and archaeological studies.