We have performed in situ quasielastic neutron scattering (QENS) measurements on zeolite-guest systems under microwave irradiation, for comparison with corresponding simulations. Both experiment and simulation reveal selective heating of methanol in silicalite, but little to no heating of benzene in silicalite. Effective translational and rotational temperatures extracted from QENS data under microwave heating were found to depend on microwave power. In agreement with simulation, QENS rotational temperatures significantly exceed translational ones at high microwave power, thus providing the first microscopic proof for athermal effects in microwave-driven nanopores.