Current assessment tools are mainly disciplinary and support the assessment of material flows in terms of environmental impacts or economical flows, for example. These tools provide helpful quantitative information for system (re)-design but do not explicitly question the value creation factors and their embeddedness in a specific socio-spatial context. This article underlines that innovation for sustainability requires more complexity and a system and multidisciplinary approach. A dynamic material and immaterial resource flows model coupled with extended scorecard to support both the analysis and structuration of territorial projects may be of great support to better understand, qualify and quantify the different kinds of resources revealed, mobilized or denied during a project. This communication focuses on the model development and the cross-fertilization of industrial, sociological and geographical disciplines for system transition analysis. Even if this model is still under development, it appears to strengthen strategic analysis, as it enables both the representation of the tangibles and intangible assets mobilized during the emergence and structuration of territorial projects (e.g. business model transition to functional economy) and sustainability assessment of existing projects (e.g. industrial and territorial ecology projects).