Understanding environmental processes at organo-mineral interfaces is crucial for assessing the retention, bioavailability, and transformation of organic contaminants and nutrients. This study investigates glyphosate, a widely used herbicide, at various organo-mineral associations, including model polysaccharide-Fe oxide and protein-Mn oxide complexes common in soils and sediments. These associations mediate critical reactions such as adsorption, desorption, and abiotic oxidation of organic constituents. Surface polarity significantly influence dissolved organic matters (DOMs) binding, kinetics, and self-assembly, affecting its conformation and other organic constituents in the system, as well. Therefore, we first examined polysaccharide adsorption-desorption behavior at water/diamond (i.e., hydrophobic) and water/goethite (i.e., hydrophilic) interfaces using in-situ ATR-FTIR/2D-COS analysis and surface wettability measurements. Both interfaces developed hydrophobicity with increasing polysaccharide loading through entropy-driven hydrophobic exclusion, Lifshitz-van der Waals forces, and H-bond formation. This suggests that organo-mineral associations create hydrophobic microenvironments that may impact the retention of organic pollutants in the soils with respect to their polarity. We observed that, plysaccharide-goethite associations reduced glyphosate adsorption (by 40-55%) and desorption (by 13-30%) at the mineral interface, revealing a complex interplay with surface polysaccharides. Weak noncovalent interactions, including hydrogen bonds and monodentate complexes, were more pronounced in the presence of polysaccharide, leading to delayed glyphosate leaching and increased bioavailability. Competitive sorption behavior of glyphosate and a model peptide at the water/goethite interface and bulk solution showed that they do not interact in solution or at the goethite surface. However, peptide modulates glyphosate retention by competing for sorption sites, influenced by hydrophobic and steric effects. We also explored glyphosate abiotic oxidation pathways on protein-Mn oxide associations using in-situ ATR-FTIR spectroscopy and LC-MS analysis. pH-induced conformational changes influenced glyphosate’s degradation, with adsorbed protein diminishing Mn oxide oxidative capacity by blocking surface sites and affecting interfacial reaction rates. Protein association reduced catalytic activity (by 22-30%) and shifted glyphosate degradation pathways, suppressing the glycine pathway by ≈55% and increasing the formation of AMPA, a toxic byproduct. This study highlights the importance of organo-mineral interactions in the retention and transformation of glyphosate, with significant implications for public health and ecosystems, where DOMs from various sources can alter glyphosate and its byproducts’ fate.