Through the use of low voltage high resolution scanning electron microscopy (LV-HRSEM) we have studied the fine details of the intricate pore structure of SBA-15. Intrawall pores and deviations from the ideal and uniform cylindrical pores are clearly observed, and we report for the first time the direct observation of “plugs” in the pores. N2-sorption measurements confirm their existence. LV-HRSEM provides an opportunity to quantify the frequency of occurrence of plugs within the pore structure. The rate of mesophase formation, followed with in situ small angle X-ray scattering (SAXS) under different solvent conditions, is shown to have a significant influence on the development of plugs and how frequently they occur. We suggest a mechanism explaining the existence of the plugs, providing means for a better understanding and control over material properties.