While the most likely structure of the active site in iron-containing zeolites has been recently identified as [FeO]2+ (Snyder et al. Nature 2016, 536, 317-321), the mechanism for the direct conversion of methane to methanol over this active species is still debatable between the direct-radical-rebound or nonradical (concerted) mechanism. Using density functional theory on periodic systems, we calculated the two reaction mechanisms over two d4 isoelectronic systems, [FeO]2+ and [MnO]+ zeolites. We found that [FeO]2+ zeolites favor the direct-radical-rebound mechanism with low CH4 activation energies, while [MnO]+ zeolites prefer the nonradical mechanism with higher CH4 activation energies. These contrasts, despite their isoelectronic structures, are mainly due to the differences in the metal coordination number and Oα (oxo) spin density. Moreover, molecular orbital analyses suggest that the zeolite steric hindrance further degrades the reactivity of [MnO]+ zeolites toward methane. Two types of zeolite frameworks, i.e., medium-pore ZSM-5 (MFI framework) and small-pore SSZ-39 (AEI framework) zeolites, were evaluated, but no significant differences in the reactivity were found. The rate-determining reaction step is found to be methanol desorption instead of methane activation. Careful examination of the most stable sites hosting the active species and calculation for N2O decomposition over [Fe]2+-MFI and -AEI zeolites were also performed.