As logistics become a substantial part of a firm's operations, the corresponding processes increases in importance. Identifying key logistics processes using a structured approach will align their outcomes to deliver the business goals, design appropriate measures and allocate sufficient resources for their improvement. This paper proposes a methodological framework for the identification, categorization and prioritization of logistics processes in the agrifood sector. Finally, a proposed mathematical model for the prioritization of logistics processes is presented. The proposed model is based on the fundamental idea of Data Envelopment Analysis (DEA) method, measuring the efficiency of the logistics processes by taking into account the multiple inputs utilised and outputs produced by them.