In recent years, several strategies have been developed and adopted in a bid to manage the biofuel supply chain. In this paper, a two-stage optimization model is proposed for integrated microalgae biofuel supply chain network design and superstructure optimization problems. In the first stage, the design of the carbon capture, utilization, and storage (CCUS) network is taken into account. A robust mixed integer linear programming (RMILP) model is proposed to optimize the strategic CCUS decisions, including the simultaneous selection of emission sources, capture facilitates, Carbon Dioxide (CO2) pipelines, intermediate transportation sites and storage sites, or microalgae cultivation sites. The second stage is dedicated to biorefinery superstructure optimization in order to determine the optimal/promising biorefinery configurations. The presented model is able to handle the inherent uncertainty of critical input parameters. Moreover, the results show that biodiesel production cost cannot compete with current diesel price, but it can be reduced significantly by improving biomass productivity.