Shrimp farming has been gaining traction in recent times due to its high value in the market as well as demand in developed nations. However, shrimp farming has recently become highly susceptible to diseases, leading to huge economic losses. The presence of antimicrobial agents in shrimp products has led to the rejection of export consignments. Thus, it has become necessary to increase the use of non-antibiotic, eco-friendly alternatives such as probiotics as a critical component of health management in shrimp culture. The popularity of probiotics is rising as a safe and environmentally friendly alternative to antibiotics in aquaculture. In recent years, the application of probiotics against bacterial diseases became a well-known approach to enhance the innate immune response of shrimp. This chapter addresses ecological concerns and the importance of maintaining a balanced microbial ecosystem in shrimp ponds with the mechanism of action of probiotics, including competitive exclusion, contribution to nutrition and digestive processes, influence on water quality, enhancement of the immune response and interference with quorum sensing for enhanced shrimp production while ensuring environmental stewardship. This article also navigates the latest methodologies and technologies employed in optimizing probiotic efficacy in shrimp culture by highlighting the potential of probiotics as an effective and sustainable strategy in aquaculture to mitigate disease outbreaks and contribute to global food security.