In drug manufacturing, solvent-based methods are used for the crystallization of active pharmaceutical ingredients (APIs). Often, the solvent interacts with the API resulting in the formation of a new solid compound, the solvate. When desolvation occurs upon heating, it might result in the formation of new solid forms with significantly different physicochemical properties. Therefore, in this work, we study the desolvation kinetics by combining in situ powder X-ray diffraction (PXRD), all-atom molecular dynamics (MD) simulations, and macroscopic solid-state reaction kinetics modeling. The fluorobenzene (FB) solvate of Bruton's tyrosine kinase inhibitor Ibrutinib (IBR) was used as a model system. While the macroscopic solid-state modeling provides information about the desolvation kinetics, the MD simulations were used to trace individual FB molecules inside the crystal lattice. The activation energy of confined solvent diffusion, obtained by MD simulations, agrees well with results of the macroscopic solid-state reaction kinetics modeling. In addition, MD simulations provided detailed information about the IBR-FB interactions at the nanoscale. The mechanism revealed is that the solvent molecules diffusion, controlled by distinct open-close gating conformational changes of the drug, triggers the desolvation throughout the crystal lattice.