For all nations as well as our planet, engineering technologies that offer the best energy alternatives to fossil fuel are needed. Among the possible alternatives, the use of agriculture and forest biomass is a key challenge requiring an approach across several scientific disciplines (biocatalysis, molecular evolution, systems biology) and areas of technical expertise (biorefinery, industrial metabolism). The bioenergy strategy, based on the optimization of both the agroresources mobilization and the industrial use of the whole plant, can be achieved through the biorefinery approach. All the carbon molecules have to be kept and the energy consumption during all the process must be as low as possible. During the last 10 years, “systems biology” became a key discipline as far as basic and medical researches are concerned. The frame of biorefinery is giving a unique opportunity for a cross-fertilization between “industrial metabolism” and “systems biology.” The biorefinery strategy can give rise to the production not only of advanced biofuel but also of bioproducts (fine chemicals, cosmetics, lubricants), agromaterials (polymers and fibers), and food ingredients. Lignocellulose deconstruction is a key issue for the actual biorefinery achievement, and there is a need for more research on biocatalysis, especially in the frame of the interaction between biocatalysis efficiency and evolution.