Apart from the academic staff ISU has a strongly radiating administrative service. At the time the university was founded it started working with one campus but later it expanded its operation with the opening the campus in Bitola and introducing new study programs. Over the years, three more faculties were opened. All these steps required new qualified staff in the administrative departments and as the new faculties were accredited the hierarchical structure of the university grew.

The structure of the university today is a result of a 15-year development path. The development was gradual, faculty by faculty, department by department. Every year the university invests in its campuses, constantly adapting them to new trends and new changes in technology. Managing such a complex system is time consuming, and therefore ISU is focused on new software solutions in order a better organization of the data to be accomplished.

The university follows the hierarchy that is presented by the Law on Higher Education of the Republic of North Macedonia. There, the main branches of the hierarchical structure are defined along with the responsibilities.  The Statute of the University is a rulebook of the university. Majority of the rules of the university are defined by the Statute of the University. Each unit of the university has to adhere to the rules provided by the Statute, but they can also be added to their own rulebooks. The roles of some of the employed (for example: the rector, the deans), the way they are elected as well as the forming of committees and other formal bodies of the university are also determined.   Also, the law suggests the minimum number of employed per faculty and the academic qualification they are obliged to have and therefore the university must abide by these rules.  Having all this information, it is understood that university will enter the process of change (at least) when the Law of Higher Education is changed and whenever a new faculty or new department is accredited.

Additionally, as the university grew, so did the need for new departments, new staff, new organizational design. Due to the rapid growth, the university has changed a lot over the years. Its structure and changes have undergone many changes. New job positions were created, and the hierarchy structure of the university opened quickly new departments. Rapid development has required very adaptive management. It is difficult to monitor the rapid growth rate, because the growth of the university does not always mean an increase in income and therefore the university management had to solve these problems. At the same time, although it invested in new buildings and staff, reorganization in all departments had to be done.

The basic structure is the same as any other university in the Republic of North Macedonia, because it is regulated by law. Professors and assistants have great autonomy in creating their lectures, as long as they are in accordance with the law, the statute, the mission, the vision and the values of the university.

In addition to the teaching process, the university has several departments, which reflect its true spirit. As it has been presented in the organogram, the university does not hire other companies for marketing, public relations, accounting, info center, IT, human resources, publishing, etc. The idea of the management is to involve as many departments in the university as possible, as this provides flexibly and easier planning. Having your own employee to perform each of the required tasks, enhances the process of gathering ideas and their realization, as opposed to the long process of hiring individual companies to operate each process separately.