Purpose Moxifloxacin (MOX) is a fourth-generation fluoroquinolone and a broad spectrum antibiotic used in the management of bacterial keratitis (BK). This investigation aimed to formulate MOX-loaded chitosan/pectin cationic polyelectrolyte nanocapsules (CPNCs) for the effective topical treatment of BK. Methods Physicochemical properties like nanocapsule size, charge, drug entrapment efficiency (EE), viscosity, pH, and in-vitro release profile of CPNCs were evaluated. The in-vitro antibacterial activity of CPNCs and marketed formulations (MFs) was studied against Staphylococcus aureus. Ex-vivo corneal permeation studies of CPNCs were evaluated with the help of a modified diffusion apparatus, which was used with goat cornea. The pharmacodynamic study was performed with optimized CPNCs on a BK-induced rabbit eye model and compared with MF. Results The optimized nanocapsules appeared as positive charge (+19.91 ± 0.66) with a nano size (242.0 ± 0.30 nm) as calculated by the dynamic light scattering method. The in-vitro release profile of CPNCs exhibited sustained release properties. The ex-vivo permeation pattern also supported the improved drug permeation through the cornea from CPNCs as compared with MF. Draize irritation studies confirmed that the prepared formulation is compatible with the corneal tissue. The in-vivo study concluded that the antibacterial activity of CPNCs was improved when evaluated with MF. Conclusion The obtained results showed that CPNCs were the better choice for the management of BK therapy due to its capability to improve the corneal adhesion of CPNCs through direct interaction with the mucous membrane of the corneal tissue.