Between 1876 and 1877 the sovereign states of Cauca and Antioquia had a warlike confrontation that contemporary historiography had studied as a civil war. Along that confrontation happened transcendental events for the political and social history of the future Republic of Colombia. In that context, this paper analyzes the incidence of Prussian education system in a representative institution such as the University of Antioquia, making an especial emphasis on the period when it was occupied to barrack troops. To unravel these facts, newspapers of the time —both liberals and conservatives— and documents from the Historical Archive of Antioquia were consulted. In the process of research, it was found unpublished information that helped to understand the educational model implemented by the conservative government of Pedro Justo Berrio, the organization and training of the troops in the University and the difficult restoration that the cloister needed to be reopened.