Nanoscale systems such as hierarchical nanoporous materials, nanosheets, and ultrathin membranes are rapidly finding increasing interest as a means of reducing transport resistance. However, the analysis of such finite-size systems is generally based on transport coefficients in bulk systems when assessing the separation performance of membrane systems, without reconciling end effects; these attenuate transport and can be governing at nanoscales. Furthermore, framework flexibility has been an open topic of discussion, especially its effect on the gas transport properties and separation factors in kinetically driven separations, but its effect in finite-size systems is largely unexplored and the underlying mechanisms still unclear. Here, we assess the gas transport limitations in finite zeolite/MOF nanosheets for flexible and rigid-averaged frameworks, using equilibrium molecular dynamics simulations to investigate the internal interfacial resistance. Three coexisting effects trigger the flexibility effect: vibrating window, thermal effect, and finite-size (entry length) effects. The last one is a function of the confinement, pore texture, and momentum accommodation on wall collision and is related to an entry region of developing flow. We find the thermal effect in the bulk system to be negligible, but in the finite system, it depends on the guest− host thermalization, with diffusion coefficients up to three times higher for CH 4 in TON zeolite and over an order of magnitude higher for CO 2 in ZIF-8. We observe that the entry length effect is present in both the flexible and rigid systems but lowered for the flexible framework. Diffusivity profiles indicate that flexibility leads to reduction in the entry length for the CH 4 /TON system and enhanced diffusivity for C 2 H 6 in TON zeolite. Our results demonstrate that the extent of flexibility effects is specific to the host− guest interactions and momentum accommodation, which are influenced by the level of confinement, pore network topology and connectivity, and generalizations require extreme caution. We find that a flexible framework allows higher diffusion coefficients and reduced transport resistances, which promote an improvement in the separation performance, and its consideration is important for realistic nanomembrane design.