Husks of rice (RH), coffee (CH), and cholupa (CLH) were used to produce natural adsorbents. The natural adsorbents were used to remove pharmaceuticals such as diclofenac, ciprofloxacin, and acetaminophen in a mixture of distilled water. However, CH stood out for its efficiency in removing ciprofloxacin (74%) due to the higher concentration of acidic groups, as indicated by the Boehm method. In addition, CH removed 86% of ciprofloxacin individually. Therefore, CH was selected and used to remove other fluoroquinolones, such as levofloxacin and Norfloxacin. Although electrostatic interactions favored removals, better removal was observed for ciprofloxacin due to its smaller molecular volume. Then, ciprofloxacin was selected, and the effect of pH, matrix, and adsorbent doses were evaluated. In this way, using a pH of 6.2 in urine with a dose of 1.5 g L−1, it is possible to adsorb CIP concentrations in the range (0.0050–0.42 mmol L−1). Subsequently, the high R2 values and low percentages of APE and Δq indicated better fits for pseudo-second-order kinetics, suggesting a two-stage adsorption. At the same time, the Langmuir isotherm recommends a monolayer adsorption with a Qm of 25.2 mg g−1. In addition, a cost of 0.373 USD/g CIP was estimated for the process, where the material can be reused up to 4 times with a CIP removal in the urine of 51%. Consequently, thermodynamics analysis showed an exothermic and spontaneous process with high disorder. Furthermore, changes in FTIR analysis after adsorption suggest that CH in removing CIP in urine involves electrostatic attractions, hydrogen bonds and π-π interactions. In addition, the life cycle analysis presents, for the 11 categories evaluated, a lower environmental impact of the CIP removal in urine with CH than for the preparation of adsorbent, confirming that the adsorption process is more environmentally friendly than materials synthesis or other alternatives of treatments. Furthermore, future directions of the study based on real applications were proposed. © 2024 Elsevier Ltd