Microorganisms are treasure and can contribute to environmental safety and sustainable development. Microorganisms can be used effectively in this context due to their astonishing metabolic activity and diverse nutritional requirements and their relationships with plants and animals. Even though microbes have caused many diseases, the main aim of this narrative review is to provide a summary of the different uses of eco-friendly microorganisms, benefits, and the expected results when using them in different applications. Originally, eco-friendly microorganisms are utilized only in organic farming, but at the moment, this is getting wider applications such as in decomposition, food production and dietary needs, sewage treatment, petroleum refining, r-DNA technology, in marine and many more. Microbial biosensors use engineered microorganisms and transducers to detect substances, emitting signals like light or electrical current. In healthcare, they hold promise for early and accurate disease detection by identifying biomarkers associated with conditions such as cancer, enabling faster and more precise diagnoses for improved patient outcomes. The establishment of a sustainable and livable ecosystem for future generations depends on the remediation and restoration of contaminated habitats utilizing efficient and environmentally friendly technology. Microbes in space face unique challenges like altered gravity and cosmetic radiation, promoting scientific exploration for their adaptability and potential implication for space missions.