Recently, supply chain risk management has been attracting growing attention. Therefore, various methods, tools, and practices have been developed in this area. However, they usually are focused on the direct consequences of disruptions occurring in supply chains. Thus, the purpose of this article is to present an operational risk analysis method for supply chains, in which consequences of an adverse event occurrence are assessed based on two measures: (1) the direct consequences (disruption) of supply processes to customers, and (2) recovery time for a supply system. Based on research findings, we introduced a Petri nets model for mapping material flows along a supply chain. We implement the proposed analysis method in a selected company from the automotive industry. The performed final discussion confirmed the relevance of distinguishing the direct and indirect consequences of the risk assessment. It was also suggested that the results’ interpretation could be two-fold, which may be necessary for appropriate risk management tool selection.