In this study, high temperature and ambient X-ray powder diffraction (XRD) are employed to differentiate the impacts of temperature and carbon deposition on the catalytic activity of the zeolite H-ferrierite (H-FER) via changes in the unit cell structure. XRD serves as a straightforward tool to distinguish these influences on the lattice geometry of H-FER, which ultimately affects catalytic activity. Due to its industrial relevance, the isomerization reaction of 1-butene to iso-butene is selected. Pristine H-FER undergoes a thermal contraction when heated from room temperature to 450 °C. However, internal carbonaceous deposits (i.e., deposits inside the micropores of the zeolite) counterbalance this effect, and the unit cell expands anisotropically during the reaction startup phase. Internal carbon deposits act as the driving force for this expansion and counteract external forces. During catalyst deactivation (time on stream >100 h), a slight unit cell contraction (i.e., ΔV = −6 Å3) is observed that stems from external carbon deposit condensation (i.e., deposits on the crystal surface). Characterization of an oxidatively regenerated catalyst supports this finding by proving this structural distortion to be nearly reversible. This study concludes that internal carbon species are primarily responsible for structural distortion and counteract thermal contraction, whereas external coke species are the driving force for catalyst deactivation.