Cork products have an increasing demand for vibration damping systems due to their good vibration isolation behavior as well as eco-friendly and sustainable properties. In this work, an improvement was proposed in the vibration attenuation behavior of multi-layer cork structures by means of two smart materials; shear thickening fluid (STF) and shear stiffening polymer (SSP). The number of layers was varied in the multi-layer cork structures while ensuring a constant thickness for the resultant composites and the smart materials were applied as film layers at the cork layer interfaces. The composites were tested in hammer-based vibration tests and the structural constants of natural frequency and damping ratio were found after modal analyses. In addition to the vibration properties, the thickening/stiffening behavior of the smart materials was also studied in rheological measurements. According to the results, the STF shows a sudden viscosity jump under increasing shear rate while the SSP changes its behavior from viscous to elastic at high rate stimulations. Due to these rheological responses, the smart materials enhance the vibration attenuation performance of the cork layers. Consequently, it is possible to state that the integration of smart materials into cork structures has a promising future to develop eco-friendly and sustainable products as well as improving adaptive properties of passive control systems in vibration damping applications.