The concept of ‘nano’ refers to the manipulation or self-assembly of individual atoms or molecular structures to create novel solutions with vastly different properties. An ecosystem is a self-contained unit of living things that includes producers (plants), consumers (animals) and decomposers (microbes). The conceptualization of ‘nano-ecosystem’ necessitates the study of microorganisms, such as bacteria, fungi and algae, at the nanoscale level within an ecosystem. It also involves the study of nanoscale interactions between microorganisms and the environment, which influences crucial environmental processes. The notion of nano-ecosystem engineering implies the deliberate manipulation and design of nano matters at an extremely smaller scale using nanotechnology. It also entails controlling and optimizing the functions of an ecosystem from nutrient cycles to the interactions between organisms. Nano-ecosystem engineering holds numerous significance in creating resilient environment which benefits both humans and the environment in the aspects of environmental sustainability by offering innovative solutions for addressing environmental challenges, such as pollution remediation, water purification and habitat restoration, optimizing resource efficiency, improving agricultural productivity, conservation of biodiversity by controlling ecosystem dynamics and other biotechnological importance that enables the development of novel techniques ranging from drug delivery to biological production. Likewise, this nano-ecosystem engineering possesses future prospectives, including medicine, environmental remediation and energy production. On the other hand, nano-ecosystem engineering grips to several challenges regarding the potential long-term impacts on ecosystems and society. This chapter will provide a comprehensive knowledge of how nano-ecosystem engineering contributes to shaping the future and the challenges evolved in it.