Antibiotics in the environment represent a substantial pollution threat. Among these emerging pollutants, ionophore anticoccidials are of special concern due to their potential ecological impact, persistence in the environment, and role in promoting antimicrobial resistance. To investigate the adsorption/desorption of the ionophore antibiotic salinomycin (SAL) on/from raw and modified clay adsorbents, batch-type experiments were performed using 0.5 g of clay adsorbent mixed with 10 mL of increasing doses of SAL solutions for each sample, at room temperature, with a contact time of 24 h. All measurements were conducted in triplicate employing HPLC-UV equipment. Three different natural (raw) and modified clay samples were investigated, which were denominated as follows: AM (with 51% calcite), HJ1 (with 32% kaolinite), and HJ2 (with 32% microcline). The experiments were carried out using three pH ranges: between 3.33 and 4.49 for acid-activated clays, 8.39–9.08 for natural clays, and 9.99–10.18 for base-activated clays. The results indicated that, when low concentrations of the antibiotic were added (from 5 to 20 μmol L−1), more than 98% of SAL was strongly adsorbed by almost all clays, irrespective of the physicochemical and mineralogical composition of the clays or their pH values. When higher SAL concentrations were added (40 and 100 μmol L−1), the adsorption of the antibiotic showed pH-dependent ligand adsorption mechanisms: (i) highly decreased as the pH raised (for the raw and base-activated AM and HJ1 clays), while (ii) slightly decreased as the pH decreased (on the acid-activated clays). Among the adsorption equations tested (Freundlich, Langmuir, and Linear), the Freundlich model was identified as the most suitable for fitting the data corresponding to SAL adsorption onto the studied clays. SAL desorption from clays was consistently below 10% for all the clay samples, especially for the acid-activated clays, due to cation bridging adsorption mechanisms, when the lowest concentration of the antibiotic was added. Additionally, it should be stressed that the desorption values can increase with rising SAL concentrations, but they always remain below 20%. Overall, the clays here investigated (both raw and modified) provide a cost-effective and efficient alternative for the removal of the veterinary anticoccidial antibiotic SAL, with potential positive and practical implications in environmental remediation and antibiotic pollution management, particularly by serving as amendments for contaminated soils to enhance their adsorption capacities against SAL. Additionally, using these clays in water treatment processes could improve the efficiency of mitigating antibiotic contamination in aquatic systems.