Most logistics organizations have some kind of process-oriented information system that keeps track of business events. Process Mining uses event logs extracted from these systems in order to discover, analyze, diagnose and improve processes, organizational, social and data structures. While there has been much research on Process Mining in the last decade, the number of studies actually demonstrating the applicability of these techniques has been limited, particularly in the field of logistics. Consequently, there is a need for real-life case studies suggesting methodologies appropriate for Process Mining analysis, especially combined with IE&M well-established methods, and displaying the benefits of its application in real-life environments. In this paper we present a methodological framework for a multi-faceted analysis of real-life event logs based on Process Mining. As such, we demonstrate the usefulness and flexibility of Process Mining techniques combined with traditional IE&M methods in order to analyze and improve the organizational process in a case study that is centered on the actual cargo release process of a large Israeli logistics company. Our analysis shows that Process Mining techniques constitute an ideal means to tackle organizational challenges by suggesting process improvements and creating a companywide process awareness.