This work describes an eco-friendly approach for in situ immobilization of Ag nanoparticles on the surface of Fe3O4 nanoparticles, with the help of Thymbra spicata extract and ultrasound irradiations, without using any toxic reducing and capping agents. The combination of Fe3O4 NPs and Ag NPs in one hybrid nanostructure (Fe3O4@T. spicata/Ag NPs) represents a promising strategy for targeted biomedical applications. The structure, morphology, and physicochemical properties were characterized by various analytical techniques such as fourier transformed infrared spectroscopy (FT-IR), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), inductively coupled plasma (ICP) and vibrating sample magnetometer (VSM). Towards the chemical applications of the material, we headed the multicomponent synthesis of diverse propargylamines by A3 coupling in water, which ended up with excellent yields. Due to strong paramagnetism, the catalyst was easily isolable and reused in 8 cycles without any leaching and considerable change in reactivity. DPPH test revealed similar antioxidant potentials for hybrid nanostructure and butylated hydroxytoluene. The hybrid nanostructure inhibited half of the DPPH molecules in the concentration of 139 µg/mL. To survey the anti-human colorectal cancer activities of the hybrid nanostructure, MTT assay was used on common human colorectal cancer cell lines. The hybrid nanostructure had very low cell viability and anti-human colorectal cancer effects dose-dependently against Ramos.2G6.4C10, HCT-8 [HRT-18], and HCT 116 cell lines. The IC50 values of the hybrid nanostructure were 289, 311, and 174 µg/mL against Ramos.2G6.4C10, HCT-8 [HRT-18], and HCT 116 cell lines, respectively. It is thought that the hybrid nanostructure obtained can be used as an anticancer drug for the diagnosis of colorectal cancer in humans after acceptance of the above findings in clinical study trials.