Implementing the multilayered structure on a stretchable platform is essential to realize a multifunctional system beyond simply imparting stretchability to a single rigid device. There have been many efforts to achieve a stretchable vertical interconnect access (VIA) for electrical connections between two or more different layers on stretchable electronics. Nevertheless, there are still challenges in implementing soft multifunctional systems with the stretchable VIA due to high complexity of the fabrication process, limitations on the circuit design, and poor compatibility with other circuit components. Here, we report a microstructured elastomer composite-based VIA that is compatible with the facile bottom-up process for multilayered structures. By applying the magnetic field to the elastomer composite of highly conductive ferromagnetic particles with core–shell structure, conductivity of the composite is greatly enhanced with filamentous structures. The design of microstructures is optimized through systematic analysis of the structural simulation and surface-strain mapping. When the substrate is stretched, microstructures efficiently disperse the mechanical stress concentrated at the interface between VIA and the substrate, which originates from the difference in Young’s modulus, resulting in the enhancement of mechanical reliability. Because VIAs and electrodes are monolithically embedded on the substrate during the process of stacking one layer on top of the underlying layer, the proposed VIA is suitable for implementing multilayered structures in a bottom-up method. To show the feasibility of our approach to multilayered stretchable electronics applications, various types of VIAs with four layers and passive matrix-stretchable LED arrays are successfully demonstrated on the stretchable platform. We believe that the proposed microstructured VIA has the potential to play a major role in paving the way toward highly integrated stretchable electronics.