This study presented the adsorption of naproxen on adsorbents filled with Cu, Fe, and Cu/Fe nanoparticles (NPs) obtained by the green synthesis method from pepper stem waste. The resulting adsorbents were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy-energy dispersive X-ray spectroscopy, and thermal gravimetric-differential thermal analysis. The amount of naproxen not adsorbed in the solution was determined from the cyclic voltammetry method, which is one of the electrochemical methods. The equation of the calibration curve used in the conversion of current to concentration and the R
2 value were
y
=
2.6165
x
−
288.22
y=2.6165x-288.22
and 0.999, respectively. While the adsorption with the BS-extract was 3.3%, it was 46.142% for Cu-NP, 92 mg/g, and 57.622% for Fe-NP. With 116.0 mg/g Cu/Fe-NP, 82.406% and 165.0 mg/g capacity were reached. In the isotherm calculations, since the R
2 values for each adsorbent were in the range of 0.998–0.997, it was determined that the Freundlich and Halsey isotherms were compatible. Accordingly, under these conditions, Naproxen adsorption was multilayered and the adsorbent surface had a heterogeneous structure. Graphs drawn from the kinetic data showed that the adsorption obeyed the second-order kinetics. The R
2 value of the kinetic curves was 1 for all adsorbents. Thermodynamic data were determined by Van’t Hoff curves with R
2 values in the range of 0.998–0.996. The enthalpy value for Cu/Fe-NP was calculated to be 31.854 kJ/mol, the entropy value was 0.1993 kJ/mol-K, and the free energy was −27.5374 kJ/mol. These values were 34.605 kJ/mol, 0.272 kJ/mol-K, and −46.451 kJ/mol for Fe-NP, respectively; and 19.79 kJ/mol, 0.247 kJ/mol-K, and −54.3226 kJ/mol for Cu-NP. While all NPs (except Cu-NP) had a high recovery percentage in three cycles, this decreased to 80% at pH 10. For Cu-NP, the recovery percentage decreased at pH 8.5 and 7, but surprisingly it increased at pH 10. As a result, it can be inferred that NPs play a good role in adsorbent development, and Fe and Cu NP-doped BS adsorbents have a better effect on naproxen adsorption and have been evaluated as adsorbents suitable for use several times.