The one-step capture of organic pollutants from water using reusable adsorbents continues to be a significant challenge for researchers in the field of water treatment. This work reports the successful design and synthesis of a new ternary polypyrrole/zirconia/chitosan (PPy/ZrO₂/Chitosan) nanocomposite, which was subsequently utilized as a promising adsorbent to capture Congo red from water. To verify the successful preparation of the nanocomposite, its chemical structure, surface morphology, and specific surface area were comprehensively investigated using multiple characterization techniques. According to adsorption experiments, the PPy/ZrO₂/Chitosan nanocomposite demonstrated enhanced performance in dye removal compared to the PPy/ZrO₂ and pure PPy. The optimization of the dye elimination process onto the nanocomposite was conducted through response surface methodology, comprehensively examining the effects of initial concentration, pH, reaction time, and temperature. Under the optimum operating conditions of contact time = 45 min, pH = 2.5, temperature = 40 °C, and initial dye concentration = 11 mg/L, the maximum Congo red removal efficiency reached 99.9%. Analysis of the experimental results under optimal conditions indicated that the kinetic behavior followed the Elovich model, whereas the Freundlich model provided the most precise fit for the adsorption isotherms. A maximum monolayer adsorption capacity of 472.28 mg/g was determined based on the Langmuir model. Adsorbent recovery experiments demonstrated high dye removal efficiency by the nanocomposite over four consecutive cycles, indicating the adsorbent’s adequate stability. Findings indicated that the successful capture of Congo red by the PPy/ZrO₂/Chitosan nanocomposite is governed by a synergistic mechanism, encompassing pore filling, Lewis acid-base attractions, π−π stacking, hydrogen bonds, and electrostatic interactions.