The use of composite materials has grown exponentially in transport structures due to their weight reduction advantages, added to their capability to adapt the material properties and internal micro-structure to the requirements of the application. This flexibility allows the design of highly efficient composite structures that can reduce the environmental impact of transport, especially if the used composites are bio-based. In order to design highly efficient structures, the numerical models and tools used to predict the structural and material performance are of great importance. In the present paper, the authors propose a multi-objective, multi-scale optimization procedure aimed to obtain the best possible structure and material design for a given application. The procedure developed is applied to an aircraft secondary structure, an overhead locker, made with a sandwich laminate in which both, the skins and the core, are bio-materials. The structural multi-scale numerical model has been coupled with a Genetic Algorithm to perform the optimization of the structure design. Two optimization cases are presented. The first one consists of a single-objective optimization problem of the fibre alignment to improve the structural stiffness of the structure. The second optimization shows the advantages of using a multi-objective and multi-scale optimization approach. In this last case, the first objective function corresponds to the shelf stiffness, and the second objective function consists of minimizing the number of fibres placed in one of the woven directions, looking for a reduction in the material cost and weight. The obtained results with both optimization cases have proved the capability of the software developed to obtain an optimal design of composite structures, and the need to consider both, the macro-structural and the micro-structural configuration of the composite, in order to obtain the best possible solution. The presented approach allows to perform the optimisation of both the macro-structural and the micro-structural configurations.