In this study, the iron-impregnated activated carbons derived from waste Citrus limetta peels (AC-CLPs) has been employed for the first time to remove the fluoride ions from water. The adsorbents were prepared by activating the selected biomass with FeCl3 and subsequent carbonization at two different temperatures 250 °C and 500 °C, and the synthesized carbon materials were designated as AC-CLP250 and AC-CLP500, respectively. The synthesized activated carbons were characterized by particle size distribution, point of zero charge (pHZPC), scanning electron microscopy (SEM), energy dispersive X-ray (EDX), Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analyses. The influence of different operating parameters including adsorbent dose, initial concentration of fluoride, contact time, solution pH and temperature on the sequestration of the fluoride ions were studied. For both carbon materials, the optimal conditions were observed as pH of 6.6, adsorbent dosage of 1.0 g L−1 and contact time of 240 min. The Langmuir and Freundlich isotherms were analyzed to understand the adsorption process on the surface of the adsorbents. Langmuir isotherm model agreed with the equilibrium data to a greater extent, indicating monolayer adsorption of fluoride ions onto AC-CLPs. The fluoride uptake capacities were found to be 4.926 and 9.709 mg g−1 by the Langmuir isotherm for AC-CLP250 and AC-CLP500, respectively. It was found that the adsorption process follows the pseudo-second-order kinetics, suggesting that the defluoridation process is chemisorption. Also, the boundary layer effect and intra-particle diffusion models were employed to scrutinize the rate-limiting step. Thermodynamic analysis revealed that the adsorption process was feasible, spontaneous, and endothermic in nature. The removal efficacy of defluoridation process was increased with increase in temperature from 25 to 45 °C. These findings provide insights to explore further the adsorption process for removal of fluoride ions using FeCl3-activated carbons derived from other agricultural wastes.