The self-diffusivity of cyclohexane and n-octane adsorbed in hierarchical zeolite monoliths has been investigated by using PFG-NMR. In these samples, the intrinsic FAU-X zeolite microporosity combines with a complex macroporous network composed of aggregated zeolite nanocrystals. As temperature is increased, cyclohexane self-diffusivity apparently decreases, reaches a minimum, and then starts increasing upon further increasing the temperature. Such striking, i.e., non-Arrhenius, temperature dependence is not observed for n-octane in the same samples and for cyclohexane adsorbed in purely microporous FAU-X. Through thermodynamic modeling, we show that this anomalous behavior can be rationalized by considering the evolution in the adsorbate populations when changing the temperature. In more detail, we show that the slow and fast diffusing species present in the microporosity and secondary porosity arising from the packing of zeolite nanocrystals vary significantly with a strong impact on the effective diffusivity. Applying the temperature evolution of their relative fractions to a simple two-phase diffusion model helps obtain insights into the physicochemical factors responsible for the complex behavior of effective self-diffusivity in hierarchical zeolites.