Commissioning is considered as a critical phase in the delivery of a Nuclear Facility (NF) as it is the first stage in the authorization of the NF to be exploited. Most of the nuclear projects start to overrun costs during commissioning mainly since this phase is not addressed properly and is affected by many issues from previous phases (Design, Procurement, and Construction). This article proposes a general methodology to prepare and realize the commissioning activities. Using models to do so improves communication and removes ambiguities between stakeholders. It also formalizes and clarifies the commissioning organization and activities prior to any implementation. It also allows for capitalizing and sharing the experience from previous projects, by drawing references models and good practices patterns. The so-called Model Based commissioning method is elaborated around concepts, languages, processes, tools, and patterns inspired from Model Based System Engineering (MBSE) principles and practices. The theoretical foundations will be supported by results from nuclear facilities demonstrating the added value.