The human gut microbiome played a major key role towards contributing essential functions to its host of an ecosystem. It refers to the entire community of microorganisms that colonize in specific locations including other microbes such as fungi, archaea, viruses, protozoans, and bacteria. The scientific community well understood that healthy gut flora is majorly responsible for the overall human health of the host. This chapter aims to explore the innovative application of nanotherapeutics in addressing two critical health challenges- gut microbiome dysbiosis and cancer apoptosis. By leveraging nanotechnology, we delve into targeted drug delivery systems that can selectively restore microbial balance in the gut and induce apoptosis in cancer cells. Through a comprehensive review of current research and advancements, this chapter will highlight the potential of nanotherapeutics in revolutionizing treatment strategies for complex diseases at the intersection of microbiology and oncology.