Soybean meal-based adhesives (SMAs) commercially applied in wood-based composites require stable bonding properties. However, the structure and properties of SMAs are not as stable as synthetic resins, which significantly affect their performances. In this study, the structure–property evolution of a SMA with working time was systematically investigated. The findings revealed that the secondary structure, microstructure, crosslinking density, zeta potential, nitrogen solubility index, viscosity, wood permeability, and bonding properties of SMA considerably vary with working time. The changes in adhesive properties were correlated with the dissolution of SM particles in crosslinker solution and the increased pre-curing of liquid SMA with working time resulting from the crosslinking reactions between the dissolved SM and the crosslinker. Preferably, SMA at the working time between 0.5 h and 3 h since the mixing of soybean meal flour with crosslinker solution, should be used in order to ensure the desired water resistance of plywood panels for engineered wood flooring. And an application strategy was proposed to ensure the required water resistance of plywood panels for manufacturing engineered wood flooring.