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Metal--organic frameworks (MOFs) are often viewed as rigid structures. However, growing experimental evidence indicates that their metal–linker connections can be quite flexible, and this flexibility could play an important role in molecular separations and catalysis. In this work, we explore how this flexibility can be induced by different guest molecules using Zr–MOF-808 as a representative system, featuring Zr6(µ3-O)4(µ3-OH)4 clusters connected by benzene-1,3,5-tricarboxylate (BTC) linkers. More specifically, we determine the free-energy changes due to guest-induced linker distortion at the nodes through enhanced-sampling simulations with a machine-learned interatomic potential (MLIP) trained on first-principles calculations. The resulting free energy surfaces show how different guests, namely methylamine, ammonia, and pyridine, influence the node–linker junctions, with the distortion mechanism and energetics depending strongly on guest size, binding strength to the Zr node, and hydrogen-bonding ability. At room temperature, methylamine binds strongly to the Zr node and induces a local distortion that is nearly reversible. The distortion is significant, involving complete cleavage of a Zr–O(BTC) bond and rotation of the BTC linker by nearly 60◦, creating an additional adsorption site at the node that can be occupied by the guest molecule. For methylamine and ammonia, the hydrogen bonds of N–H⋯O(BTC) steer the distortion by pulling the linker away from the node. However, pyridine, which is larger and lacks such an H-bonding interaction, must overcome a high free energy barrier to distort the MOF; only at 373 K do entropic effects make the distorted state accessible. Such detailed analysis of guest adsorption in flexible frameworks at finite temperature, rather than in rigid zero-temperature models, has been made possible by the use of advanced sampling techniques together with MLIPs. To the best of our knowledge, our findings provide a first detailed, dynamic view of the molecular processes that underlie linker distortion across multiple adsorbates in a Zr MOF, and serve to provide a mechanistic basis for tuning the flexibility of the framework through the control of the steric and electronic properties of guest molecules.