This comprehensive study investigated mechanical and thermal properties, and biodegradability of bioepoxy/clay nanocomposites based on soybean oils in line with their morphological structures and clay dispersion. Bioepoxy/clay nanocomposites were fabricated using a solution casting method according to the preferred combination of factors predetermined from our previous Taguchi design of experiments (DoEs). The effect of material formulation in terms of contents of epoxidized soybean oil (ESO) and Cloisite 15 clays, and curing agent type was of particular interest in this study. A typical mix of partial clay intercalation/exfoliation and clay aggregation was clearly observed in such bionanocomposites, irrespective of different material formulations in use. The increase in ESO content demonstrated significant enhancements in both impact strength and biodegradability when compared to those of conventional nanocomposites. However, tensile properties, hardness, and thermal properties of bionanocomposites conversely declined accordingly, arising from the plasticization effect of ESO to produce flexible biodegradable materials with less brittle nature.