Holonic Manufacturing Systems (HMS) was first proposed as a new manufacturing paradigm at the beginning of 1990 and has subsequently received a lot of attention in academic and industrial research. The application of holonic concepts to manufacturing was initially motivated by the inadequacy of existing manufacturing systems in the following two aspects: (i) dealing with the evolution of products within an existing production facility, and (ii) maintaining a satisfactory performance outside of normal operating conditions. In spite of the large number of developments reported in Holonic Control Architectures and Holonic Control Algorithms, there is very little work reported on Methodologies for HMS. Manufacturing requirements impose significant properties on HMS making the modelling process of HMS a complex and difficult task. In this work we describe how to engineer Holonic Manufacturing Systems using a Multi-agent System method. Our approach is based on holonic systems specific requirements, and it incorporates software engineering principles in order to assist the system designers at each development stage. It implements a collaborative-engineering process for HMS, and provides clear and unambiguous analysis and design guidelines.