This study reports the valorization of pistachio shell agricultural waste, aiming to develop an eco-friendly and cost-effective biosorbent for cationic brilliant green (BG) dye adsorption from aqueous media. Pistachio shells were mercerized in an alkaline environment, resulting in the treated adsorbent (PSNaOH). The morphological and structural features of the adsorbent were analyzed using scanning electron microscopy, Fourier transform infrared spectroscopy, and polarized light microscopy. The pseudo-first-order (PFO) kinetic model best described the adsorption kinetics of the BG cationic dye onto PSNaOH biosorbents. In turn, the equilibrium data were best fitted to the Sips isotherm model. The maximum adsorption capacity decreased with temperature (from 52.42 mg/g at 300 K to 46.42 mg/g at 330 K). The isotherm parameters indicated improved affinity between the biosorbent surface and BG molecules at lower temperatures (300 K). The thermodynamic parameters estimated on the basis of the two approaches indicated a spontaneous (ΔG < 0) and exothermic (ΔH < 0) adsorption process. The design of experiments (DoE) and the response surface methodology (RSM) were employed to establish optimal conditions (sorbent dose (SD) = 4.0 g/L and initial concentration (C0) = 10.1 mg/L), yielding removal efficiency of 98.78%. Molecular docking simulations were performed to disclose the intermolecular interactions between the BG dye and lignocellulose-based adsorbent.