This work aimed to describe the adsorption behavior of Congo red (CR) onto activated biochar material prepared from Haematoxylum campechianum waste (ABHC). The carbon precursor was soaked with phosphoric acid, followed by pyrolysis to convert the precursor into activated biochar. The surface morphology of the adsorbent (before and after dye adsorption) was characterized by scanning electron microscopy (SEM/EDS), BET method, X-ray powder diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR) and, lastly, pHpzc was also determined. Batch studies were carried out in the following intervals of pH = 4–10, temperature = 300.15–330.15 K, the dose of adsorbent = 1–10 g/L, and isotherms evaluated the adsorption process to determine the maximum adsorption capacity (Qmax, mg/g). Kinetic studies were performed starting from two different initial concentrations (25 and 50 mg/L) and at a maximum contact time of 48 h. The reusability potential of activated biochar was evaluated by adsorption–desorption cycles. The maximum adsorption capacity obtained with the Langmuir adsorption isotherm model was 114.8 mg/g at 300.15 K, pH = 5.4, and a dose of activated biochar of 1.0 g/L. This study also highlights the application of advanced machine learning techniques to optimize a chemical removal process. Leveraging a comprehensive dataset, a Gradient Boosting regression model was developed and fine-tuned using Bayesian optimization within a Python programming environment. The optimization algorithm efficiently navigated the input space to maximize the removal percentage, resulting in a predicted efficiency of approximately 90.47% under optimal conditions. These findings offer promising insights for enhancing efficiency in similar removal processes, showcasing the potential of machine learning in process optimization and environmental remediation.