The aim of this study is to improve the methodology for assessing the level of sustainable development of a transport enterprise, as well as to develop a project and mechanism for integrating the strategy of sustainable development as one of the functional strategies of the marketing management concept for harmonizing interests with stakeholders. To achieve the set goal, a number of modern interdisciplinary research methods and techniques were used, including abstract-logical methods such as analysis and synthesis, induction and deduction; generalization - for reviewing information sources, studying domestic and foreign experience; systemic analysis - for a comprehensive understanding of the research object and a complex analysis of relationships between elements within the defined problem as a whole; problem-oriented approach - for scientific justification of the methodology for assessing the level of sustainable development of a transport enterprise. The study discusses widely accepted methodological approaches to assessing sustainable development, one of which was taken as a basis, slightly modified and supplemented with indicators reflecting the content of the marketing management concept, taking into account the interests of stakeholders, and improved in terms of mathematical logic. It was proposed to distinguish a separate component of sustainability – risk sustainability, which generally refers to the internal property of a system that contributes to preserving its integrity in the face of various disruptive influences from the external and internal environment. Furthermore, based on the improved methodology for assessing the level of sustainable development of a transport enterprise, a project "Designing Sustainable Development of a Transport Enterprise" has been launched. Its goal is to integrate the principles of the concept of sustainable development into the enterprise's marketing management system. The implementation of the developed functional strategy for managing the sustainable development of a transport enterprise is based on the Balanced Scorecard toolkit, which allowed presenting goals for each area of sustainable development in the form of a hierarchy and decomposition, aligning general and specific interests, taking into account the interests, goals of the enterprise, and key stakeholders. Measures were also taken, including the use of marketing communication tools, for reflexive interaction with stakeholders, operational controlling to align interests, processes, and goals of marketing management. The theoretical conclusions, approaches, and recommendations proposed in the article can be used to assess the level of sustainable development of a transport enterprise and to implement a mechanism for integrating the strategy of sustainable development and the marketing management system based on the Balanced Scorecard toolkit and controlling to harmonize the goals of market-oriented enterprise management and the goals, interests of key stakeholders.