Bio-farming is a chemical-free agricultural system for improving soil health which ultimately increases crop production. For sustainable agriculture, the soil microbiome is crucial for promoting soil fertility plant growth. The use of beneficial microbes as bio-fertilizers is of utmost importance in agriculture because of their potential impact on crop production and food safety. Some naturally occurring microbes include bacteria (growth-promoting rhizobacteria and cyanobacteria), fungi, and other beneficial microorganisms. The implication of microorganisms leads to the enrichment of nutrients, proper water absorption, boosting plant growth, and increase plant tolerance ability against biotic and abiotic factors. The application of beneficial microorganisms would play a key role in protecting the environment as eco-friendly and cost-effective inputs for the farmers. The advantages of beneficial microbes support farmers to use bio-fertilizers and biocontrol agents as well as minimize the overuse of harmful chemical fertilizers and pesticides. This chapter focuses on the significant role of beneficial microorganisms as bio-fertilizers and biopesticides in sustainable agriculture enhancing overall crop performance as well as protection.