The main objective of this article is to introduce an open‐source, online software tool called OMAT as a teaching tool for performing economy wide‐material flow analysis (EW‐MFA) at urban or regional level in industrial ecology curricula. To that intent, we present a classroom and project activity that was developed for a masters‐level industrial ecology course offered by the Autonomous University of Barcelona. Insights are provided with regards to the outcome of the classroom exercise as well as lessons learned from both an academic and a software development point of view. The OMAT software provides users with a specialized tool to enter and process MFA data in a simple, intuitive way. The usefulness of OMAT as a teaching tool was tested by engaging students in a classroom activity that entailed using OMAT as a tool to perform an EW‐MFA applied to the Metropolitan Area of Barcelona for the years 2005‐2011. The aim of this exercise was to teach students specific skills required in performing an EW‐MFA, not through theory classes, but hands‐on through a learn‐as‐you‐go approach. The exercise not only equipped the students with knowledge about MFA, but also introduced them to solving problems as a team, meeting project deadlines, and communicating effectively with colleagues from different disciplines and backgrounds. Even though there is room for further improvements, this exercise showed that OMAT provided a useful addition to traditional methods that allowed students to get a more practical and thorough understanding of the MFA methodology.