The management of applied research projects requires an organized and efficient methodology to manage economic resources, establish clear and achievable objectives and balance the competitive demands of different stakeholders. In Colombia there are programs that support social investment projects, which have very demanding requirements and controls, being a challenge for higher education institutions. This article describes the experience of the research group GIBIC in the management of applied research projects in the health sector, using a methodology based on PMI, obtaining results that have exceeded expectations.