<p>Magnetotactic bacteria (MTB) produce the biogenic nanoparticles (NPs) made up of magnetite (Fe₃O₄) and gregite (Fe₃S₄). The biogenic NPs also known as magnetosomes have great importance in biomedical sciences for application such as magnetic hyperthermia, MRI, and targeted drug delivery. However, the issue lies in the obtaining an axenic culture of MTB and magnetosomes. To overcome this issue, attempts were made to develop an MTB consortium and extract biogenic NPs for further use in magnetic hyperthermia. The sediment samples were used to develop an MTB consortium. The extracted NPs were characterized based on their magnetic properties such as Vibrating sample magnetometer (VSM), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy with Energy Dispersive X-ray spectroscopy (SEM-EDAX), and Transmission Electron Microscopy (TEM) with size of 40.44&#xa0;nm. The analysis of 16&#xa0;S amplicon sequencing revealed that the consortium had a high abundance of <i>Bacillus</i>, followed by <i>Magnetococcus</i>,<i> Microvirga</i>, <i>Elusimicrobium</i>, and <i>Desulfovibrio.</i> An in vitro study of tissue-mimicking phantom for application in magnetic hyperthermia was carried out using different concentrations of magnetosomes (0.5-1.0&#xa0;mg/ml). Further, the nanotoxicity of magnetosomes was evaluated in in vivo model of nematode <i>C. elegans</i>. Different assays such as biodistribution assay to study iron uptake, oxidative stress assay, pharyngeal pumping rate assay, and lyso-tracking were performed to evaluate nanotoxicity. The obtained results demonstrated that magnetosomes at a concentration of 0.95&#xa0;mg/ml were suitable to elicit hyperthermic response with good amount of ROS generation and non-toxic too.</p> Graphical Abstract <p></p>