The JBLF Maritime University's vision of becoming the leading institution in Quality Education and Training through Total Quality Management drives the top management to go beyond quality. in 1996, the school invested in quality management system by certifying with DNV Rules for Maritime Academies and Training Centers making the institution the first maritime school in the Philippines with a certified quality management system. Further, in 2001, the school was certified to ISO 9001:1994.

During the first decade of the century, other quality management system evolved such as the Envrionmental Management System (ISO 14001), Occupational Health, Safety and Security (OHSAS 18001:2004)  among others. These paved the way to the plan of the institution to integrate various standards into JBLFMU Quality Management System.

On May 15, 2013, the Chariman of the Board of Trustees, Dr. Mary Lou L. Arcelo, contracted Capt. Kjell Johansen, Norwegian consultant, to provide consultancy services to the university on the areas of Quality, Health, Safety and Environment in order to elevate the level of the University Quality Management System to comply with the European Foundation Quality Management (EFQM) Excellence Model. The new thrust of the university will qualify graduates of JBLFMU to board European fleet in case the EMSA audit for the Philippines fails. The integration pfr safety, health, and environment in the current quality system will become the new JBLFMU QHSE Management System. This calls for the creation of the QHSE Team composed of teh QA Mangers of the three academic units and the training center, and teh QA Manager Coordinators as team players. The QHSE team is to be led in by the System Quality Assurance Internal Auditor while Capt. JOhansen acts as the consultant. The QHSE project commenced May 15, 2013 to end May 14, 2014. The success of the project lies on the participation and support of everyone in the JBLF Community.