Epoxy resin (EP) is widely used in coatings, adhesives, and molding materials. EP's high crosslinking density provides a strong modulus but also leads to reduced elongation at break and lower toughness. In this study, bacterial cellulose microgel (BC‐M) is employed to toughen EP through in situ polymerization, to form an interpenetrating network with EP. Bacterial cellulose nanofibers (BC‐CNF) and ethylated bacterial cellulose microgels (EM) are used as controls to highlight the advantages of the 3D network in enhancing polymer toughness. BC‐M demonstrates the most effective toughening performance for EP. At a filler content of 0.3 wt.%, BC‐M/EP nanocomposites exhibite significant improvements in mechanical properties, including a fracture strength of 107.8 MPa, strain of 3.53%, Young's modulus of 3.09 GPa, and toughness of 1.98 kJ m−3. Compared to EP, these values represent enhancements of 40%, 9.5%, 27.3%, and 58.4%, respectively. Comparisons with BC‐CNF/EP and EM/EP nanocomposites clearly demonstrate that BC‐M provided superior toughening effects. The exceptional toughening capability of BC‐M is attributed to its 3D network structure, which effectively dissipates applied energy, and its strong interfacial interaction with the epoxy matrix through covalent bonding.