Microbe-related, especially viral-related pandemics have currently paralyzed the world and such pathogenesis is expected to rise in the upcoming years. Although tremendous efforts are being made to develop antiviral drugs, very limited progress has been made in this direction. The nanotheranostic approach can be a highly potential rescue to combat this pandemic. Nanoparticles (NPs) due to their high specificity and biofunctionalization ability could be utilized efficiently for prophylaxis, diagnosis and treatment against microbial infections. In this context, titanium oxide, silver, gold NPs, etc. have already been utilized against deadly viruses like influenza, Ebola, HIV, and HBV. The discovery of sophisticated nanovaccines is under investigation and of prime importance to induce reproducible and strong immune responses against difficult pathogens. This review focuses on highlighting the role of various nano-domain materials such as metallic NPs, magnetic NPs, and quantum dots in the biomedical applications to combat the deadly microbial infections. Further, it also discusses the nanovaccines those are already available for various microbial diseases or are in clinical trials. Finally, it gives a perspective on the various nanotechnologies presently employed for efficient diagnosis and therapy against disease causing microbial infections, and how advancement in this field can benefit the health sector remarkably.