Nowadays, the concept of innovation is omnipresent in political and economic discourses and in technological, socio-economic and scientific development plans. This returns to the fundamental role of innovation in solving complex problems in a revolutionary way that helps lead countries to development and prosperity. The realization of an innovation is not the result of a random act, but the result of a process rich in scientific and technical tools and methods using material and human resources. These human resources must possess specific technical and transversal innovation skills. These competencies are reflected in the competence frameworks for engineering education, which increasingly emphasize the need to train creative and innovative engineers capable of succeeding in major development projects. To this end, engineering education, whether in engineering schools or universities, must manage and structure the resources and activities needed to promote innovation in a well-defined process. Thus, the objective of this work is to propose a systemic modelling of the process of realization of an innovative project in the training of engineers. To do this, case studies were conducted in an engineering school in Morocco. This involves studying innovative projects for implementing an "ISO 14001" environmental management system in an engineering school. These studies identify several elements that characterize the innovation process such as: input elements, output elements, control milestones and resources. The added value of this research work is the understanding of the complexity of the innovation system in the context studied through its representation. This will facilitate the identification of barriers to innovation in engineering education and help put in place an appropriate action plan to promote innovation and creativity.