This work focuses on the impact of covalent organic frameworks' (COFs) pore flexibility in the adsorption and separation of benzene and cyclohexane. With this aim, we have selected the imine-linked 3D COFs COF-300 and LZU-111 as examples of flexible and rigid frameworks, respectively. Optimized syntheses at room temperature or in solvothermal conditions enabled us to selectively isolate the narrow-pore form of COF-300 (COF-300-rt) or a mixture of the narrow-pore and a larger-pore form (COF-300-st), respectively, with different textural properties (BET specific surface area = 39 or 1270 m 2 /g, respectively, from N 2 adsorption at 77 K). In the case of LZU-111, only the room temperature route was successful, leading to the known microporous framework. COF-300-rt, COF-300-st, and LZU-111 were studied for benzene and cyclohexane adsorption and separation in static and dynamic conditions. At 298 K and 1 bar, these COFs adsorb more benzene (251, 221, and 214 cm 3 /g STP, respectively) than cyclohexane (175, 133, and 164 cm 3 /g STP, respectively). Moreover, the benzene and cyclohexane isotherms of COF-300-rt and COF-300-st are characterized by steps, as expected with a flexible material. Indeed, in situ powder X-ray diffraction experiments on benzene-and cyclohexane-impregnated batches enabled us to trap, for the first time, a sequence of forms of COF-300 with different pore aperture, rationalizing the stepped hysteretic isotherms. Finally, benzene/cyclohexane separation was evaluated using a benzene/cyclohexane 50:50 v/v flow at different temperatures (T = 298, 323, and 348 K): LZU-111 does not selectively retain any of the two components, while COF-300 exhibits stronger benzene−COF interactions also in dynamic conditions.