In order to deal with global competition, industries have undertaken many efforts directed to improve manufacturing efficiency. From a broad perspective, two possible approaches are the adoption of lean manufacturing methodologies or the implementation of information tools: for several years, these two approaches have been assumed to be mutually exclusive. The present work aims to define a methodology to support developers and practitioners in the integration of Manufacturing Execution Systems with the lean manufacturing approach. A case-study in the field of aeronautics is presented to validate the method.