Shigella flexneri is one of the principal cause of bacillary dysentery and contributes significantly to the worldwide implication of diarrheal infections. The presence and upsurge of multidrug resistance amongst Shigella strains, demands additional genetic analyses, advancement of new/improved drugs, and finding vaccine candidates against the pathogen. Whilst many features about the invasion of colonic cells by Shigella have been identified, fundamental gaps in information concerning in what way the bacteria transit, survive, and control gene expression, remain. Present study aims to illustrate the role of yfiB gene in Shigella virulence, which is a part of the periplasmic YfiBNR tripartite signaling system. This system is responsible for regulating cyclic-di-GMP levels inside the bacterial cells, which is a vital messenger molecule impacting varied cellular processes involving biofilm formation, cytotoxicity, motility, synthesis of exopolysaccharide, and other virulence mechanisms like adhesion and invasion of the bacteria. Through a combination of genetic, biochemical, and virulence assays, we show how knocking out the yfiB gene can disrupt the entire YfiBNR system and affect biofilm formation, bacterial invasion, surface attachment, and the virulence of Shigella. We then show how targeted mutagenesis of the significant amino acids of the YfiB protein can affect the proper functioning of the protein. This study eventually improves our understanding of the in-vivo persistence and survival of Shigella and provides a prospective new target to design anti-infective drugs and vaccines against S. flexneri and other bacterial pathogens.