In Colombia 17% of the Universities have high quality accreditation, these being the Higher Education Institutions HEI, more competitive and of quality in the market, all of them favored by an Integral Management System -IMS, which allow to establish their policies and achieve their objectives. Then the question arises: how could the administration of HEI be improved? Thus, the objective of this Investigation is to analyze the importance of IMS in modern management, as well as how IMS affect the strategic institutional direction. The results present a methodology to implement the IMS and make it integrate with the Higher Education Quality Assurance System -SACES. The following studies relate to the way of continuing integrating other systems of management, one presents of conclusive form the integration to the SIG of the management of the Investigation, development and innovation I+D+I through the NTC 5801 standard, case Universidad Militar Nueva Granada -UMNG.