Water-based coating has gained much attention globally due to environmental issues. This work aims to develop a waterborne epoxy coating incorporated with modified natural rubber (NR) latex for improved performance. For this purpose, the NR latex was modified into three types of low molecular weight epoxidized natural rubber (LENR) latex. The waterborne epoxy resin was prepared by simply mixing the epoxy resin with an amine curing agent in water and various LENR latex contents (10 to 50 wt%). The waterborne epoxy/LENR blend was coated on a tin substrate and the cured coating demonstrated better adhesion and bending properties than the neat epoxy. Phase morphological properties displayed a rough surface with a heterogeneous surface structure of the dispersed rubber and epoxy matrix. Two glass transition temperatures were observed, corresponding to the rubber modifier and the epoxy matrix. The mechanical properties of the thermosetting epoxy/LENR blends were assessed, revealing a maximum increment in elongation ability by approximately 370% for adding 50 wt% LENR, compared to the neat epoxy. These results hold the potential avenue for utilizing NR-based material in the waterborne epoxy-based resin for coating applications. Furthermore, it contributes to the NR, a renewable and eco-friendly material, in the coating technology, embracing a sustainable future.