Ordered nanoporous materials including zeolites, zeotypes, and metal‐organic frameworks (MOFs) are widely used in the fields of heterogeneous catalysis, ion exchange and gas storage/separation. In addition, due to their particular structural features new applications are continuously being explored as a consequence of their well‐defined porous network, thermal stability, acidity and guest‐species confinement. All physicochemical properties are directly structure related and therefore characterization at atomic level is highly desired. In the current work, we have aimed to review the recent progress of electron microscopy science applied to the characterization of different nanoporous materials since the first work that made use of spherical aberration (Cs) corrected electron microscopy in 2010. All difficulties encountered for the application of this technique will be presented, together with the excellent degree of information that can be extracted and the scientific responses that only Cs‐corrected electron microscopy can provide in the area of nanoporous materials, zeolites, zeotypes and MOFs.