In supply chain management, random events can occur that are difficult to predict. Once such event, the COVID-19 pandemic, affected supply chains around the world and forced companies to make sudden changes. Companies could still operate and deliver their products to customers through innovation, but also through the flexibility and innovation of transport enterprises. In the last two decades, the Polish transport industry has gained importance in the European Union. The main objective of this paper is to determine the specification of business operations under pandemic conditions, assess the impact of the pandemic on international transport SMEs in Poland, and then identify key challenges for the industry from the point of view of entrepreneurs. To this end, a literature review, desk research and snowball sampling were carried out towards the end of 2021 and beginning of 2022. The research results show that changes in the organisation of supply chains, diversification, changes in demand and other effects of the pandemic have had a positive impact on the operations of some transport companies in Poland, and the larger the company, the more these changes have been used in a positive way for the business operations of transport. This seems to be confirmed by statistical data. The biggest beneficiaries of the changes seemed to have been medium-sized and large companies. Micro enterprises, on the other hand, most often assessed the impact of the pandemic negatively. In addition, the challenges relating to the amount of fines in transport, indicated most often in our survey by the entrepreneurs, certainly also hit the micro-enterprises the hardest.