The serious toxicological effects of heavy metal ions in aquatic ecosystems have motivated the search for alternatives to reduce contamination of water sources from industrial wastewater. In this work, continuous adsorption of nickel, cadmium, and lead was assessed using a packed bed column filled with Cocoa (Theobroma cacao L.) pod husks widely available in the northern region of Colombia. The physicochemical characterization of the agricultural biomass was performed to quantify its chemical composition by bromatological, FT-IR, and energy-dispersive X-ray spectroscopy (EDS). The breakthrough curves were constructed for all heavy metal ions with bed depth of 4 and 7.5 cm, taking aliquots at 10, 30, 60, 90, 120, 150, 180, 210, 240, and 270 min. Moreover, experimental data were fitted to adsorption models in continuous mode to predict adsorptive performance (Adams–Bohart, Thomas, and Yoon–Nelson). For the FT-IR analysis of biomass before and after adsorption, the most representative bands occur around 3200–3900 cm−1 attributed to the presence of hydroxyl groups, showing the destruction of the peaks of lignocellulosic materials. The breakthrough curves revealed that for a 7.5 cm bed, adsorption performance reported the following order of promising results: Pb2+ > Ni2+ > Cd2+; while for a 4 cm bed, Pb2+ > Ni2+. The mechanism of adsorption of the evaluated metals onto cocoa pod husk was attributed to cationic exchange and microprecipitation due to the presence of Ca, K, and Si in the structure of the bio-adsorbent. Finally, the continuous adsorption was modeled under the mathematical expressions of Adams–Bohart, Thomas, and Yoon–Nelson reporting good fitting with correlation coefficient above 0.95.