During the last thirty years the level of interest in Complexity Science has been constantly increasing. Combining the opportunity offered by the findings of the Complexity Science with the framework of the multi-disciplinary debate on the meaning and use of diagrams, we propose a design methodology to help designers support their interventions in complex environments. The structural features analysis of Complex Systems has been our key point to outline this methodology to offer designers a new mindfulness in the use of design tools. This methodology is based on five phases: analysing, representing, pinpointing, timing and telling. It provides a theoretical framework that incorporates many tools suggesting a different use of them with a special attention to improve the designer's consciousness of the system he is designing in. When design is addressing complexity, diagrams could become generative tools that can be used to produce metadata relevant to the design process.