Floods often occur in agricultural areas during the rainy season and cause crop failure of agricultural commodities. Not only the farmers but the country’s economy will also be affected due to rising food prices due to product scarcity. Beneficial microbes can help reduce flood stress damage to crop plants. These microbes include mycorrhizae, plant growth-promoting rhizobacteria, and endophytes. Each type of microbe can be used as a bio-inoculant and helps reduce stress levels with various mechanisms. Bio-inoculant technology can be used as an alternative solution to help reduce the adverse effects of flood stress on crop plants. In addition, the use of bio-inoculants is also environmentally friendly because it does not damage the soil structure and can even help increase soil nutrients which can support the growth of crop plants. The potential utilization of microbes or bio-inoculants has not been clearly explained. It needs to be studied further. In this chapter, the potential of microbial utilization to lower flood stress damage of crop plants is discussed.