Microalgae are sunlight-driven micro-organisms that convert carbon dioxide into valuable molecules of interest (i.e. lipids, proteins, carbohydrates and pigments) for a broad range of industrial applications such as energy, food, cosmetics and pharmaceuticals. They offer many advantages such as a rapid growth rate, a greenhouse gas fixation ability and high biomass and lipid productivities. Microalgae oil is therefore considered as a promising alternative energy source to fossil fuels. However, despite these advantages, several scientific, technological and economical bottlenecks remain in the different steps of the production, particularly in the culturing (growth and productivity) and downstreaming. Those must be overcome to envision the feasibility of large-scale production of algae-based biofuels. In the particular case of downstream processing (extraction and pretreatments), the very robust cell walls of microalgae influence significantly the efficiency. The development of alternative systems such as those based on microalgae-bacteria co-culturing techniques represent a great potential, with enhanced growth rates and lipid yield. Besides, we hypothesize a consequent effect on the cell wall structure and thus extraction efficiency. MicroPILOTING project deals with designing and developing a microfluidic platform to study the growth of bacteria and the growth and lipid productivity of microalgae in different co-culturing conditions. A predictive quantitative growth model involving iterative optimizations, will be established to investigate the mutual dependencies of the growth of microalgae and bacteria., via the production of CO2, O2 and vitamin B12. Such microfluidic tools combined with mathematical analysis, is very original, and will permit the determination of the best culturing and pretreatment conditions, thus improving the performance for conversion efficiency, and cost reduction for obtaining in-fine low-cost bioenergy carriers.