In this study, we present the synthesis of a novel peptide-based magnetogel obtained through the encapsulation of γ-Fe2O3-polyacrylic acid (PAA) nanoparticles (γ-Fe2O3NPs) into a hydrogel matrix, used for enhancing the ability of the hydrogel to remove Cr(III), Co(II), and Ni(II) pollutants from water. Fmoc-Phe (Fluorenylmethoxycarbonyl-Phenylalanine) and diphenylalanine (Phe2) were used as starting reagents for the hydrogelator (Fmoc-Phe3) synthesis via an enzymatic method. The PAA-coated magnetic nanoparticles were synthesized in a separate step, using the co-precipitation method, and encapsulated into the peptide-based hydrogel. The resulting organic/inorganic hybrid system (γ-Fe2O3NPs-peptide) was characterized with different techniques, including FT-IR, Raman, UV-Vis, DLS, ζ-potential, XPS, FESEM-EDS, swelling ability tests, and rheology. Regarding the application in heavy metals removal from aqueous solutions, the behavior of the obtained magnetogel was compared to its precursors and the effect of the magnetic field was assessed. Four different systems were studied for the separation of heavy metal ions from aqueous solutions, including (1) γ-Fe2O3NPs stabilized with PAA, (γ-Fe2O3NPs); (2) Fmoc-Phe3 hydrogel (HG); (3) γ-Fe2O3NPs embedded in peptide magnetogel (γ-Fe2O3NPs@HG); and (4) γ-Fe2O3NPs@HG in the presence of an external magnetic field. To quantify the removal efficiency of these four model systems, the UV-Vis technique was employed as a fast, cheap, and versatile method. The results demonstrate that both Fmoc-Phe3 hydrogel and γ-Fe2O3NPs peptide magnetogel can efficiently remove all the tested pollutants from water. Interestingly, due to the presence of magnetic γ-Fe2O3NPs inside the hydrogel, the removal efficiency can be enhanced by applying an external magnetic field. The proposed magnetogel represents a smart multifunctional nanosystem with improved absorption efficiency and synergic effect upon applying an external magnetic field. These results are promising for potential environmental applications of γ-Fe2O3NPs-peptide magnetogels to the removal of pollutants from aqueous media.