In this work, a novel adsorbent (MIL-100-Fe-AMSA), for the removal of the nonsteroidal anti-inflammatory drug sodium diclofenac (DCF), was prepared by grafting aminomethanesulfonic acid to the open iron sites in a porous MIL-100-Fe MOF obtained by a green microwave-assisted synthesis. The obtained materials were characterized by XRD, N2 adsorption-desorption, FTIR spectroscopy of adsorbed CO, electron microscopy and EDS spectroscopy. MIL-100-Fe-AMSA showed fast adsorption kinetics and an excellent maximum adsorption capacity of 476 mg/g. Synergistic effect of H-bonding, between the electronegative ionized –SO3H groups of MIL-100-Fe-AMSA and –NH group of DCF, and π−π interactions between the aromatic rings that are present in both MOF and pollutant, is probably the main mechanism of adsorption. In addition, the developed functionalized-MOF showed excellent reusability for at least five consecutive adsorption-desorption cycles, demonstrating its stability and potential for the removal of DCF. For practical applications, the prepared MIL-100-Fe-AMSA was incorporated into a 3D printed column for flow-through solid-phase extraction of pharmaceuticals pollutants before HPLC determination. The functional device showed excellent performance for the preconcentration and further detection and quantification of ketoprofen and DCF pollutants.