Cancer remains the second leading cause of death worldwide even though advances in early diagnosis and treatment are being actively pursued. Nanoparticles (NPs) are one of the most widely studied materials in the recent decade and are emerging as promising agents in the cancer management. Pertinent to realizing this truth, toxicity issues related to nanoproducts are of particular concern that is often ignored. Nanostructures synthesised using materials of biological origin using eco-friendly ‘green’ chemistry approach, partially addresses this problem. Biologically synthesised NPs are accounted for various applications in cancer management such as bioimaging, drug delivery, sensitising, photothermal and photodynamic therapy and so on. Cancer stem cells (CSCs) are a small population of extremely tumourigenic and intrinsically drug resistant cells that are responsible for the tumour initiation, progression, resistance, and relapse. In addition to small molecules and nucleic acid-based therapeutics, combining nanomaterials with antibodies against CSC-specific markers or CSC-targeting agents have been engaged for the selective targeting and developing of anti-CSCs therapeutics. Yet despite the benefits reaped by the NPs, in the overall management of complex diseases like cancer, disadvantages such as toxicity and pollution inevitably follow. The first part of this review essentially budges on the application of NPs produced using ‘green’ biological materials, which are poised to dissipate some of the issues. The latter half is aimed to discuss the utility of nanoparticles in CSC-targeted therapies.