Autonomy as a fundamental guarantee for the implementation of educational activities accompanied the formation of the first universities, subsequently acquiring regional specificity. The education system in Russia objectively operates by a different structure for the interrelation of the subjects and mechanisms in order for educational organizations to implement their activities compared to the era of the first universities. In the article, the authors identify and propose to consider the key nodes of the legal status of universities: organizational and legal form as a legal shell, proprietary rights in property, methods of financing, tax preferences, and forms of control over activities. The study of these features is important for answering the questions of whether they lead to the emergence of a new model of legal regulation of universities and whether there is a correlation with university autonomy. Both answers, as shown in the article, are negative. The decision should not come only "from above", although the state recognition of the independence of universities should be expressed in the expansion of their powers in property and financial spheres. Educational organizations themselves must realize the value of autonomy, starting with the formulation of their mission, which is presented formally and not meaningfully in the charters of Russian universities. The mission of the article's authors is seen in the ability to make independent decisions and be responsible for such decisions. The participation of a public entity in the functioning of universities today seems to be excessive: goal setting, state task, and state control should not suppress the autonomy of educational organizations. The use of various public resources may become a Solomon solution: supervisory and board of trustees, student government, internal financial audit, and others. Finally, the latest and far from the last challenges to the education system (digitalization, pandemic) are shifting the area of responsibility to the universities themselves, which will have to make operational decisions based on their vision of the current situation. For this to occur, educational organizations need to understand the degree of their autonomy.