The modern stage in the development of the transport industry is characterized by changes in the traditional economic models of interaction between multiple participants in the provision of transport and logistics services. These changes are caused by digital technologies that form a new digital outline of the business models of the transport industry. The digital ecosystem of transport and logistics is the basis for the breakthrough development of the Russian economy and increasing its competitiveness. However, the digital update format does not offer ready-made solutions, its deployment is constrained by the lack of the necessary number of competent personnel, the high cost of implementing and maintaining digital tools, ensuring high reliability, data preservation and security. All this requires additional resources to overcome the emerging barriers with minimal losses. In this regard, the study of the stated topic is demanded and relevant. Therefore, the purpose of the current study is to systematize the main challenges that create imbalances in the pace and scale of modification of the digital circuit of the transport and logistics ecosystem of the Russian Federation. The need to systematize the challenges in creating the digital contour of the transport and logistics ecosystem is justified by the presence of multiple economic interests in this area, including socially significant ones. However, their multidirectional and contradictory nature hinders the rate of formation of a single trend of development of the transport complex and logistics activities of all participants providing services, as well as the creation of a single digital platform that accumulates the potential for effective interaction of transport complex operators. The study was conducted using general scientific methods of knowledge, such as: generalization and systematization of scientific and statistical data on the risks of the barrier environment in the digital transformation of the Russian transport industry, forming the main challenges of the digital ecosystem of transport and logistics, their comparative analysis, synthesis, application of systemic and functional approaches.