The present study analyzed Medicago sativa L. crops irrigated by TiO2 in the anatase phase and TiO2 doped with Ag, Fe, Cu ions at 0.1%w synthesized by the sol-gel method (SG) and the sol-gel coupled with microwaves (Mw-SG). The materials were added to the irrigation water at different concentrations (50, 100, and 500 ppm). Affectation levels were observed by measuring stem morphology, chlorophyll content, secondary metabolite content (total phenolic, flavonoids), and antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl radical assay. The results revealed a reduction in stem and leave size at different concentrations and chlorophyll content, showing no correspondence with the applied dose. Nanostructured materials in the soil generated nitrogen, boron, and potassium deficiencies observed in leaves. No linear effect related to the increase in total gallic acid, rutin content, and antioxidant activity dependent on concentration was determined. The stress factor depended on the dopant type, generating different stress levels at the three organs investigated (leaves, roots, stem). The metabolite augmentation was mainly obtained at 100 and 500 ppm for both synthesis methods.