In response to extension of coverage goals in higher education, academic programs offering has been growing in regions geographically dispersed which management requires solid information systems able to adapt to the context needs and particularities. This paper presents a descriptive case study conducted in one of the head offices of Corporación Universitaria Minuto de Dios operating in 34 municipalities of cundinamarca department in colombia, highlighting challenges evidenced in the process of design and implementation of a custom ERP system. The case of study provides wide contextual details about selection and design of components, customization, integration and evaluation of the ERP system. Through this analysis are documented (a) the challenges in integration, escalability and interoperability of ERP systems in higher education that are evidenced in a context of regionalization with geographic dispersion variables; and (b) the differential features provided by a custom ERP system respect to the currently used systems in higher education.