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Monodispersed highly magnetic iron oxide nanocubes and nanospheres with magnetization (78.72 emu/g_cubic and 72.08 emu/g_sphere with an average size of 17.45 ± 5.13 nm for spherical (IONPs) and with edge lengths ranging from 20.85 ± 6.60 nm for nanocubes (IONCs) have been successfully synthesized and functionalized with methoxy-polyethylene glycol (m-PEG). The specific absorption rate (SAR) has been observed to be 351.5 W/g for IONPs and 415.06 W/g for the IONCs. The antimicrobial activity of the synthesized nanoparticles (NPs) against Staphylococcus aureus and Escherichia coli was evaluated using the agar well diffusion method. Anti-angiogenic effects were evaluated via the Chick Chorioallantoic Membrane (CAM) assay, an extensively used in vivo model. Additionally, m-PEG-coated IONCs were functionalized with doxorubicin (DOX) and the tumor-targeting aptamer AS1411 to enable targeted magneto-chemotherapy (MCT) in 3D breast cancer models. The results show that magneto-chemotherapy (MCT) reduces cancer cell viability to 76.41% in 2D cultures and 77.27% in 3D cultures, highlighting the potential of 3D models for enhancing the effectiveness of targeted therapies in breast cancer.