Lightweight structures are widely used across different industry sectors. However, they get easily excited by external influences, such as vibrations. Undesired high vibration amplitudes can be avoided by shifting the structural eigenfrequencies, which can be achieved adapting the structural design considering optimisation procedures and structures primarily inspired by diatoms. This procedures has been applied to the development process of a girder structure installed in a synchrotron radiation facility to support heavy magnets and other components. The objective was to design a 2.9 m long girder structure with high eigenfrequencies, a high stiffness and a low mass. Based on a topology optimisation result, a parametric beam–shell model including biologically inspired structures (e.g., Voronoi combs, ribs, and soft and organic-looking transitions) was built up. The subsequent cross-sectional optimisation using evolutionary strategic optimisation revealed an optimum girder structure, which was successfully manufactured using the casting technology. Eigenfrequency measurements validated the numerical models. Future changes in the specifications can be implemented in the bio-inspired development process to obtain adapted girder structures.