In this study, a new eco-friendly kaolinite–cellulose (Kaol/Cel) composite was prepared from waste red bean peels (Phaseolus vulgaris) as a source of cellulose to serve as a promising and effective adsorbent for the removal of crystal violet (CV) dye from aqueous solutions. Its characteristics were investigated through the use of X-ray diffraction, Fourier-transform infrared spectroscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and zero-point of charge (pHpzc). The Box–Behnken design was used to improve CV adsorption on the composite by testing its primary affecting factors: loading Cel into the composite matrix of Kaol (A: 0–50%), adsorbent dosage (B: 0.02–0.05 g), pH (C: 4–10), temperature (D: 30–60 °C), and duration (E: 5–60 min). The significant interactions with the greatest CV elimination efficiency (99.86%) are as follows: BC (adsorbent dose vs. pH) and BD (adsorbent dose vs. temperature) at optimum parameters (A: 25%, B: 0.05 g, C: 10, D: 45 °C, and E: 17.5 min) for which the CV’s best adsorption capacity (294.12 mg/g) was recorded. The Freundlich and pseudo-second-order kinetic models were the best isotherm and kinetic models fitting our results. Furthermore, the study investigated the mechanisms responsible for eliminating CV by utilizing Kaol/Cel–25. It detected multiple types of associations, including electrostatic,n-π, dipole–dipole, hydrogen bonding interactions, and Yoshida hydrogen bonding. These findings suggest that Kaol/Cel could be a promising starting material for developing a highly efficient adsorbent that can remove cationic dyes from aqueous environments.