In this work, we demonstrate the potential of bi-directional structural optimization (BESO) for the design of multi-resonant microsystems. BESO belongs to the family of topology optimization (TO). Opposed to classical design optimization based on the variation of geometrical dimensions, TO allows for more fundamental design changes. For this demonstration, we apply BESO on two microelectromechanical systems: a linear gyroscope and a mircromirror with two rotational degrees of freedom. For the design optimizations, we target specific resonant behavior, i.e., desirable resonance frequencies and their respective amplitudes, for each device according to its functionality. We achieved multi-resonant designs that exhibit the specified resonant behaviors and resemble rather biological shapes than typical rectangular MEMS geometries. This demonstrates the potential of BESO to complement current design strategies.