We have performed molecular dynamics (MD) simulations of zeolite-guest systems driven by microwaves (MW), to study how energy is distributed in these systems as a function of guest loading. Expanding on a previously published communication [Blanco, C.; Auerbach, S. M. J. Am. Chem. Soc. 2002, 124, 6250.], we have found that MW-driven MD with the Andersen thermostat gives robust steady states, while MW-driven MD with the Nose-Hoover chain thermostat does not. We studied MW-driven zeolites NaY, DAY and silicalite, as well as benzene and/or methanol in DAY or silicalite. DAY and silicalite exhibit little MW heating, while NaY gives strong MW heating primarily through the Na cations, whose kinetic energy was found to equilibrate on picosecond time scales. Zeolite-benzene systems show minimal MW heating, while zeolite-methanol systems exhibit significant MW heating with steady-state temperatures increasing linearly with methanol loading. MW-driven equimolar mixtures of benzene and methanol at low to medium loadings in DAY or silicalite obey T-methano much greater than T-benzene > T-zeolite, suggesting that MW heating of binary mixtures in zeolites can produce novel effects. However, MW-driven MD at higher loadings shows that T-methanol similar to T-benzene > T-zeolite, suggesting that closely related MW sorption studies can produce markedly different results viz. athermal effects.