Digital modelling of manufacturing systems is experiencing a fast development, but it still shows significant limitations when considering integration and interoperability of enabling technologies. Indeed, there is still a lack of reference integrated workflows to perform the wide span of tasks, ranging from layout configuration and performance evaluations to 3D representations. Commercial software tools are either too complex or expensive to be approached by non-specialists, therefore it is hard to design effective learning activities in manufacturing system engineering. This paper proposes a structured learning workflow based on an open toolkit that takes advantage of a common ontology-based data model to smoothly integrate digital tools for manufacturing system modelling, performance evaluation, and virtual reality representation. After detailing methodologies and digital tools, the proposed workflow is applied to a pilot case in higher education. © 2022 The Society of Manufacturing Engineers