Magnetite nanoparticles (NPs) possess properties that make them suitable for a wide range of applications. In recent years, interest in the synthesis of magnetite NPs and their surface functionalization has increased significantly, especially regarding their application in biomedicine such as for controlled and targeted drug delivery. There are several conventional methods for preparing magnetite NPs, all of which mostly utilize Fe(iii) and Fe(ii) salt precursors. In this study, we present a microwave hydrothermal synthesis for the precipitation of magnetite NPs at temperatures of 200 °C for 20 min and 260 °C for 5 min, with only iron(iii) as a precursor utilizing chamomile flower extract as a stabilizing, capping, and reducing agent. Products were characterized using FTIR, PXRD, SEM, and magnetometry. Our analysis revealed significant differences in the properties of magnetite NPs prepared with this approach, and the conventional two-precursor hydrothermal microwave method (sample MagH). FTIR and PXRD analyses confirmed coated magnetite particles. The temperature and magnetic-field dependence of magnetization indicate their superparamagnetic behavior. Importantly, the results of our study show the noticeable cytotoxicity of coated magnetite NPs—toxic to carcinoma cells but harmless to healthy cells—further emphasizing the potential of these NPs for biomedical applications.