The ability of peptides to form stable complexes with metal ions offers a remarkable starting point for elaborating catalysts and antibacterial agents.This paper reports the synthesis and characterization of a new inexpensive organometallic-montmorillonite as highly active catalyst and antibacterial agent. An Fe(II)-Glycylglycylglycine (Fe-3Gly) complex was covalently anchored to montmorillonite K10 (K10) previously grafted with 3-aminopropyl-trietoxisilane (APTES). Multiple techniques were used to investigate the different steps of functionalization, to name FTIR, TGA, XRD, N2 adsorption–desorption technique, RD/UV–Vis, and SEM-EDS. The catalytic activity of the prepared catalyst was determined in terms of decolorization efficiency percentages of Congo Red dye (CR) in an aqueous solution using three types of Advanced Oxidation Processes (AOPs) that are the heterogeneous Fenton, the photocatalysis and photo-Fenton processes. A full factorial design of experiment was established in the photo-Fenton process in order to i) identify the most influential parameters and their interactions, and ii) determine the experimental conditions most favorable to the degradation. Thus, five factors were considered: catalyst weight (X1), H2O2 volume (X2), pH (X3), CR concentration (X4) and time (X5). From the statistical analysis, the correlation coefficient for the model was R2 = 0.90 and the most effective factor in the photo-Fenton degradation efficiency was the pH. The experimental values fitted with the predicted ones, thereby indicating the appropriateness of the established model. Furthermore, the prepared material showed good antibacterial activities.