Logistics companies that unite supply chains participants are trying to seek for effective tools and use them for sustainable development based on introduction of progressive forms and methods of flow processes. The paper justified the concept of economic sustainability in respect to logistics companies and identified factors contributing to their adaptation and sustainable development under modern conditions. The authors outlined the following trends, priorities and results of innovative development of supply chains within sustainable development: use of digital technologies based on big data and analytics, as well as machine learning, artificial intelligence, supply chains hyper-automation, etc. All this is an indisputable factor to improve efficiency of not only logistics companies, but also the country’s GDP in general. Requirements for digital activity and logistics companies’ transformation in order to achieve social, environmental and economic sustainability of logistics systems are explained in this work. Thus, introduction of innovative technologies in order to control flows contributes to a preventive approach to identify bottlenecks while implementing logistics functions that can lead to an increase in economic sustainability. While achieving social sustainability, digital transformation improves labor conditions of logistics workers. Use of innovative eco-technologies within logistics companies makes it possible to increase their competitiveness and minimize negative impacts on the environment. The research also examined experience of the functioning of successful logistics companies as part of the strategy of sustainable development in supply chains.