Green synthesis is a viable alternative for creating nanoparticles from environmentally friendly sources. Sonchus asper extract was used in this study to prepare ZrO2 nanoparticles that can adsorb amoxicillin from an aqueous solution as a reducing and stabilizing agent. The complex product was synthesized and then annealed for four hours at 500 °C, 600 °C, and 700 °C to produce fine ZrO2 powder. X-ray diffraction, BET, FTIR, and TEM were employed to explore these samples' structural characteristics. Structural analyses showed that a cubic phase with slight size variation at different annealing temperatures is present in nanocrystalline ZrO2 powder. We examined the influence of initial amoxicillin concentration, pH, and temperature on amoxicillin adsorption. Compared with other widely popular materials used to remove amoxicillin, the zirconia produced in this study had a much better adsorption capability. The adsorption processes were spontaneous and endothermic, following thermodynamic characteristics, including standard enthalpy change (H), Gibb's free energy change (G), and standard entropy change (S). The green production method and zirconia nanoparticles are promising to adsorb a developing contaminant.