Natural bio-surfactants have recently attracted much more attention due to their biodegradability and biocompatibility. They are often associated with clay materials to synthesize organoclays and can therefore be ideal materials for environmentally friendly oil-based drilling fluids. In this study, a bio-organoclay was obtained by modifying bentonite with natural soybean lecithin, and the effects of reaction temperature, time, pH, and lecithin concentration on the properties of modified bentonite were analyzed. Structural insights such as clay properties, intercalation process and lecithin organization were obtained using a large variety of experimental techniques and molecular dynamics simulations. The results of this study suggest that some experimental conditions have an important impact on the basal space of the bentonite. Reaction time and temperature did not have a significant effect on the final properties of the modified bentonite. However, by increasing the pH of the clay material or with a high concentration of lecithin, the interlayer space fluctuates from 1.21 to 5.96 nm. The lecithin molecules adopt a new spatial conformation in the interlayer space becoming perpendicular to the clay surface, which largely increase the interlayer space