In this study, a novel approach to toughen biobased epoxy polymer with different types of siloxanes was explored. Three different modified siloxanes, e.g., amine-terminated polydimethyl siloxane (PDMS-amine), glycidyl-terminated polydimethyl siloxane (PDMS-glycidyl), and glycidyl-terminated polyhedral oligomeric silsesquioxane (POSS-glycidyl) were used as toughening agents. The curing and kinetics of bioepoxy was investigated by differential scanning calorimetry and Fourier transform infrared spectroscopy. The mechanical, thermal, and morphological properties of the cured materials were investigated. Rheological characterization revealed that the inclusion of POSS-glycidyl slightly increased the complex viscosity compared to the neat resin. The morphology of the cured bioresin was characterized by transmission electron microscopy and scanning electron microscopy. The inclusion of POSS-glycidyl to bioepoxy resin resulted in a good homogeneity within the blends. The inclusion of PDMS-amine or PDMS-glycidyl was shown to have no effect on tensile and flexural properties of the bioresins, but led to a deterioration in the impact strength. However, the inclusion of POSS-glycidyl enhanced the impact strength and elongation at break of the bioresins. Dynamic mechanical analysis showed that the siloxane modified epoxy decreased the storage modulus of the bioresins. The thermal properties, such as decomposition temperature, coefficient of linear thermal expansion, and heat deflection temperature were improved by inclusion of POSSglycidyl.