Developing immersive learning systems is challenging due to their multidisciplinary nature, involving game design, pedagogical modelling, computer science, and the application domain. The diversity of technologies, practices, and interventions makes it hard to explore solutions systematically. A new methodology called Multimodal Immersive Learning Systems Design Methodology (MILSDeM) is introduced to address these challenges. It includes a unified taxonomy, key performance indicators, and an iterative development process to foster innovation and creativity while enabling reusability and organisational learning. This article further reports on applying design-based research to design and develop MILSDeM. It also discusses the application of MILSDeM through its implementation in a real-life project conducted by the research team, which included four initiatives and eight prototypes. Moreover, the article introduces a unified taxonomy and reports on the qualitative analysis conducted to assess its components by experts from different domains.