The present study aimed to synthesize iron oxide nanoparticles loaded with quinine and alkaloids-rich Cinchona officinalis (Peruvian bark) stem bark extract, and further evaluate their cytotoxic effect and apoptosis mechanisms in MCF-7 breast cancer cells. Nanoparticles were prepared by biological reduction of iron oxide with Cinchona officinalis extract, using the green synthesis method. The nanoparticles were characterized by XRD, FT-IR, and UV-vis spectroscopy and transmission electron microscopy (TEM). In vitro cytotoxicity analyses of Cinchona officinalis extract, ferrous oxide, and Cinchona officinalis extract-loaded iron oxide nanoparticles (CO-NPs) were carried out using the MTT test for 24 h and 48 h. We found that CO-NPs reduced the MCF-7 cell viability with IC(50) values of 16.2 and 9 microg/mL in 24 h and 48 h, respectively. In addition, CO-NPs were tested with normal hMSCs to determine their toxicity, and we did not find noticeable cytotoxicity. Confocal fluorescent microscopy revealed that CO-NPs efficiently increased the nuclear condensation and chromatin damage in propidium iodide staining; meanwhile, there was decreased mitochondrial membrane potential in CO-NPs-treated MCF-7 cells. In addition, AO-EB staining confirmed the late apoptotic and apoptotic morphology of cancer cells. Further gene expression analysis confirmed that the upregulation of tumor suppressors, Cdkn1A, Prb, and p53 was significantly increased, and inflammatory traits such as TNF-alpha and Nf-kappab were increased in cancer cells treated with CO-NPs. Apoptotic stimulators such as Bax and caspase-3 expression were highly significantly increased, while mdm-2 and Bcl-2 were significantly decreased. Overall, the enhanced cytotoxic potential of the Cinchona officianlis stem bark extract loaded CO-NPs versus free Cinchona officianlis extract might be due to the functional stabilization of bioactive compounds, such as alkaloids, quinine, flavonoids, phenolics, etc., into the iron oxide, providing bioavailability and internalization of cinchona metabolites intracellularly.