This article explores the impact of nano-silica on the properties of woven flax fibre/epoxy composites. Using compression moulding, epoxy/flax/silica hybrid nanocomposites were produced. The nano-silica was dispersed in the epoxy matrix via ultrasonication at various weight ratios. A series of tests, including crack durability, dynamic mechanical analysis, and scanning electron microscopy, were conducted to evaluate the modified materials. Notably, a 3% nano-silica filler load resulted in a 54% and 57% improvement in initiation and transmission interfacial fracture toughness, respectively. Scanning electron microscope imaging confirmed that fibres pull out at the crack tip during initial debonding, accounting for the increased toughness. Dynamic mechanical analysis further revealed enhancements in mechanical properties. Moreover, the 3% nano-silica content led to less fibre pull-out, suggesting higher heat resistance than standard flax/epoxy composites. The material also demonstrated promising antimicrobial efficacy against gram-positive and gram-negative bacteria, offering a potential alternative to conventional antibiotics.