Zeolites are becoming more versatile in their chemical functions through rational design of their frameworks. Therefore, direct imaging of all atoms at the atomic scale, basic units (Si, Al, and O), heteroatoms in the framework, and extra-framework cations, is needed. TEM provides local information at the atomic level, but the serious problem of electron-beam damage needs to be overcome. Herein, all framework atoms, including oxygen and most of the extra-framework Na cations, are successfully observed in one of the most electron-beam-sensitive and lowest framework density zeolites, Na-LTA. Zeolite performance, for instance in catalysis, is highly dependent on the location of incorporated heteroatoms. Fe single atomic sites in theMFIframework have been imaged for the first time. The approach presented here, combining image analysis, electron diffraction, and DFT calculations, can provide essential structural keys for tuning catalytically active sites at the atomic level.