Cork-based composite structures reinforced with shear thickening fluids (STFs) have demonstrated significant potential in impact mitigation due to their unique combination of sustainability and enhanced mechanical properties. These hybrid materials capitalize on the inherent properties of cork in addition to the dynamic response of STFs and have demonstrated promising results for the mitigation of impact forces. This study investigates the development and application of STFs within cork composite structures for impact mitigation. Utilizing polyethylene glycol (PEG) with a molecular weight of 200 g/mol and fumed silica nanoparticles, various STF formulations were synthesized and characterized. Rheological properties of the STFs were analyzed, focusing on the shear thickening behavior with silica concentrations ranging from 10 to 60 wt.%. The formulated STFs were integrated into agglomerated cork composites, forming layered structures subjected to 20 J impact tests. The results indicated that silica concentrations higher than 30 wt.% resulted in crystallization, rendering them unsuitable for further rheological analysis. Only silica concentrations of 10 wt.% in PEG 200 exhibited typical shear thickening behavior, while concentrations of 20 and 30 wt.% demonstrated to be unstable. However, all samples containing STF demonstrated higher strain energy densities, indicating better energy absorption capacity. Despite the limitations, the findings suggest that STFs within cork layers can effectively enhance energy absorption during impacts, and new composite configurations should be further explored.