The competitiveness of companies in emerging countries implies many European countries must transform their production systems to be more efficient. Indeed, the new context created by the COVID-19 pandemic increases the necessity of digital transformation and focuses attention on its limited uptake by manufacturing companies. In France, the Industry 4.0 concepts are already implemented in large companies. Despite the demonstration and validation of their benefits, SMEs are reluctant to move towards implementation. This problem of SME performance improvement increases with the current geopolitical situation in Europe (raw materials and gasoil cost). It is thus urgent and paramount to find a better solution for encouraging SMEs in their transformation. Taking note of the brakes on uptake of Industry 4.0 concepts in SMEs, the objectives of this paper are to find levers to accelerate implementation of Industry 4.0 concepts in SMEs, through the development and the deployment of a sustainable Industry 4.0 methodology, and to develop an intelligent system for supporting companies’ digital transformation in order to improve their performance. After a literature review, focused on Industry 4.0 concepts, theory of systems, organizational methods, and artificial intelligence, a sustainable methodology will be presented. The SME performance model that has been elaborated will then be shown and the structure of the intelligent system (mainly the decision aided tool) being developed for supporting the digital transformation of SMEs will be described. An illustrative example relating to a food elaboration SME will be presented for validating the concepts that have been developed. The proposed framework helped the company to formulate guidelines and transition towards a sustainable 4.0 company.