In the paper, the impact of the COVID-19 virus is analyzed on the basis of professional literature on transport, but also on transport during the pandemic, using example of transport modalities. It tries to answer the questions of how the pandemic affected and which branch had the most transport of goods compared to others. The transport modalities and modern transport technologies that are necessary for the efficient operation of each modality, their operation during the pandemic and protection measures are described. Air, road, rail and sea transport are compared, with a focus on freight transport exclusively in the European Union and the Republic of Croatia. Research shows that the pandemic has affected all the mentioned branches of transport. Furthermore, the increase in transport is observed in rail transport. Further research emphasizes the importance of personnel protection and restrictions in all transport modalities that are considered necessary, in order to prevent the spread of infections with as little economic loss as possible. It is then observed that restrictions and measures affect the delivery of goods in supply chains. Ultimateley, restrictions and measures lead to shortages of food commodities as well as medical supplies. The next negative effect on the delivery of goods is a delivery delay. Another reason for the delay in the delivery of goods is the spread of the infection, the obervance of measures and the lack of the necessary workforce. The aim of this paper is to show the negative impact of the pandemic on transport modalities and to find solutions that arose due to the pandemic.