This book chapter focuses on novel innovative strategies for the prevention and treatment of various types of zoonotic diseases like viral, bacterial, fungal, parasitic, mycoplasma, protozoal and chlamydial infections. The treatment and diagnosis of zoonotic infections are challenging due to drug resistance, genetic mutations and modification of target sites. Therefore, more effective and low-cost theranostics tools are needed to manage the emerging zoonotic infections. Nano-formulations have many advantages over conventional medicines which are used in the treatment of zoonotic infectious diseases by delivering targeted drug delivery, minimizing drug resistance, and causing less toxic effects. Enormous developments have been prepared in manufacturing innovative nano-formulations to control zoonotic diseases based on the usage of mannose-linked thiolated nanocarriers, arginine-based nanocarriers, mannosylated thiolated chitosan (MTC)-coated PM-loaded PLGA NPs, adjuvant pDNA hydrogel, poly (ethylenimine) conjugated nanomicelles and quantum dots to diagnose and treat a huge range of zoonotic infections for examples rabies, tuberculosis, zoonotic influenza, lyme diseases, salmonellosis, leishmaniasis, brucellosis, other emerging infections caused by coronaviruses (COVID-19, MERS, SARS) and West Nile virus in a specially targeted way. The controlled delivery and targeted antimicrobial drugs for treating and diagnosing zoonotic infections via binding to the overexpressed infectious macrophages are the revolutionized development in medicine by nanotechnology. Nano-vaccines and theranostic solicitations of nanoformulation have significant therapeutic potential to combat diverse microbial pathogens. Nanorobots and biocompatible nanoparticles are the nanoscale materials that are used in nanomedicine for the purposes of sensing, diagnosis and drug delivery in the living organism. This chapter reviewed innovative strategies to control zoonotic diseases and future perspectives by using nanotechnology.