In the current study, the mechanistic understanding of the adsorption isotherm and thermodynamic aspects of cationic methylene blue (MB) dye adsorption onto cellulosic olive stones biomass from wastewater were investigated. The batch adsorption of MB onto the olive stones (black and green olive stones) was tested at a variety of pH, dye concentrations, temperatures, and biomass particle sizes. The adsorption thermodynamics such as Gibbs free energy, enthalpy, and entropy changes were also calculated. Moreover, the desorption studies of MB from the spent olive stones were studied to explore the re-usability of the biomasses. The results revealed that under the optimum pH of 10, the maximum MB uptake was achieved i.e. 80.2% for the green olive stones and 70.9% for the black olive stones. The green olive stones were found to be more efficient in remediating higher MB concentrations from water than the black olive stones. The highest MB removal of the green olive stones was achieved at 600 ppm of MB, while the highest MB removal of the black olive stones was observed at 50 ppm of MB. Furthermore, for almost all the concentrations studied (50–1000 ppm), the MB adsorption was the highest at the temperature of 45 °C (P value < 0.05). It was shown by the Fourier transform infrared that the electrostatic interaction and hydrogen bonding were proposed as dominant adsorption mechanisms at basic and acidic pH, respectively. While the hydrophobic-hydrophobic interaction was a dominant mechanism at neutral pH. The thermodynamic studies revealed that the adsorption process was endothermic, spontaneous, and favorable. Moreover, the real wastewater experiment and the desorption studies showed that the green and black olive stones were a cost-effective and promising adsorbents for MB remediation from wastewater on account of their high adsorption and desorption removal capacities.