Liver transplantation (LT) is a critical intervention for end-stage liver disease, while complications, such as infections, graft rejection, and metabolic disturbances are common post-transplant. The gut microbiota-bile acid (GM-BA) axis plays a pivotal role in regulating liver function and overall health, influencing both the gut microbiota and bile acid metabolism. This review explored the complex interplay between the gut microbiota (GM) and bile acids during liver transplantation. It also discussed how disruptions in this axis can lead to post-transplant complications, such as infection, rejection, and liver injury. Specifically, the role of microbiota-derived bile acids was assessed in shaping immune responses and metabolic pathways that may impact liver graft function. Furthermore, therapeutic strategies aimed at modulating the GM-BA axis were reviewed to improve post-transplant outcomes, including the use of probiotics, prebiotics, and bile acid receptor modulators. Understanding the mechanisms behind GM-BA dysregulation may provide new directions for improving liver transplant survival and reducing complications.