A series of organoclays were synthesized by modifying bentonite with lecithin under two pH reaction solutions, one acid and one basic. The products prepared using various surfactant concentrations (0.2–5.0CEC) were characterized by multiple experimental techniques. The conformational arrangement of the loaded surfactant, as well as the fluctuation in lecithin molecular properties and interlayer cation content in the organoclay were evaluated. According to the experimental results, the conformation of lecithin in the organoclay interlayer space undergoes a transition from flat-lying layer to a tilted paraffin-type-bilayer. This phenomenon happens for both pH but, interestingly, follows two different mechanisms. It can be observed that the cations content decreased during the addition of lecithin at pH = 1.0, suggesting that the surfactant intercalated into the interlayer space through cation exchange. On the contrary at pH = 9.0, the zwitterionic nature of lecithin allowed its intercalation in the interlayer space via ion-dipole interactions with the cations. Compared with the organoclay prepared at pH = 1.0, the organoclay prepared at pH = 9.0 also exhibited weaker hydrophobicity, clearly reflecting the difference in the interlayer conformation.