Farnesoid X receptor (FXR) is a nuclear receptor with an essential role in regulating bile acid synthesis and cholesterol homeostasis. FXR activation by agonists is explained by an αAF‐2‐trapping mechanism; however, antagonism mechanisms are diverse. We discuss microsecond molecular dynamics (MD) simulations investigating our recently reported FXR antagonists 2a and 2 h. We study the antagonist‐induced conformational changes in the FXR ligand‐binding domain, when compared to the synthetic (GW4064) or steroidal (chenodeoxycholic acid, CDCA) FXR agonists in the FXR monomer or FXR/RXR heterodimer r, and in the presence and absence of the coactivator. Our MD data suggest ligand‐specific influence on conformations of different FXR‐LBD regions, including the α5/α6 region, αAF‐2, and α9‐11. Changes in the heterodimerization interface induced by antagonists seem to be associated with αAF‐2 destabilization, which prevents both co‐activator and co‐repressor recruitment. Our results provide new insights into the conformational behaviour of FXR, suggesting that FXR antagonism/agonism shift requires a deeper assessment than originally proposed by crystal structures. Molecular dynamics simulations indicate a ligand‐specific influence on conformations of different FXR‐LBD regions, such as αAF‐2 and the heterodimerization interface (α9‐ α11). Changes in the heterodimerization interface seem to be coupled with αAF‐2 destabilization, which prevents recruitment of co‐regulatory elements. These results give insight into the conformational behaviour of FXR, suggesting that FXR antagonism/agonism shift requires a deeper assessment than originally proposed by crystal structures.