High performance polymers with bio-based modifiers are promising materials in terms of applications and environmental impact. In this work, raw acacia honey was used as a bio-modifier for epoxy resin, as a rich source of functional groups. The addition of honey resulted in the formation of highly stable structures that were observed in scanning electron microscopy images as separate phases at the fracture surface, which were involved in the toughening of the resin. Structural changes were investigated, revealing the formation of a new aldehyde carbonyl group. Thermal analysis confirmed the formation of products that were stable up to 600 °C, with a glass transition temperature of 228 °C. An energy-controlled impact test was performed to compare the absorbed impact energy of bio-modified epoxy containing different amounts of honey with unmodified epoxy resin. The results showed that bio-modified epoxy resin with 3 wt% of acacia honey could withstand several impacts with full recovery, while unmodified epoxy resin broke at first impact. The absorbed energy at first impact was 2.5 times higher for bio-modified epoxy resin than it was for unmodified epoxy resin. In this manner, by using simple preparation and a raw material that is abundant in nature, a novel epoxy with high thermal and impact resistance was obtained, opening a path for further research in this field.