This research presents a review of context in the field of computer security about document management systems; in turn it generates an alternative process design and IT development, which permits the effective incorporation of multi-factor strong authentication services and confidentiality to a document management system, focused on security of electronic documentation. They worked with officials from the University ofthe Llanos, so that the requirements were accurate and then to test the system in a simulated scenario; with three modules load of documents and biometric fingerprint systems.For this, performance tests were applied, always focusing on security.