The article presents a methodology for assessing the level of formation professional competencies in university digital environment. The proposed methodology includes principles that should be taken into account when assessing learning outcomes in the digital environment, a three-step approach to building the educational process using adaptive e-learning course (AELC), and a model for assessing the formation of professional competencies in AELC. The scientific novelty of the methodology is constructing a model that includes formalizing the structure of an adaptive e-learning course and means of assessing labor functions: knowledge, skills and labor actions according to the cognitive, praxiological and motivational/axiological components of competency. The formalization of the structure and evaluation tools of the adaptive e-learning course was carried out to assess the results of the formation of professional competencies. Formulas are proposed for assessing professional competency for individual modules of the discipline, for the discipline and for the educational program as a whole, implemented in digital environment. The results of testing the methodology for assessing the formation of professional competencies in teaching students of the direction of training “Information Systems and Technologies” in School of Space and Information Technologies of Siberian Federal University are presented. The approach allows us to minimize the subjectivity of the teacher in assessing student learning outcomes, and also allows for automated assessment of the level of formation professional competencies in the digital environment and, according to the new education standards (FSES 3++), provides sufficient objectivity in assessing formation level. In the future, the proposed method can be extended to estimate the level of formation of universal and general professional competencies of the curriculum and to become the universal tool to assess the level of training of the graduates.