The mechanisms of formation of organically modified (phenyl, vinyl, and methyl) silica materials with cubic Pm3̅n and hexagonal p6m periodic mesostructures obtained in one step in the presence of the cetyltrimethylammonium bromide (CTA+B) surfactant are reported in this study. Understanding the way these complex materials form is difficult but undoubtedly necessary for controlling the material structure and its properties because of the combined presence of surface organic groups and large surface areas. Here, the mechanism of formation is clarified on the basis of the modeling of time-resolved in situ small angle X-ray scattering (SAXS) experiments, with a specific focus on the micelle evolution during material formation. Their fast self-assembly is followed for the first time with a quick temporal resolution of a few seconds using a third-generation synchrotron radiation source. To better understand the behavior of the complex organic-containing mesostructure, we perform a comparative study with the corresponding organo-free, isostructural materials obtained from three different surfactants (CTA+, CTEA+, and CTPA+) having a constant chain length (C16) and an increasing polar head volume (met-, et-, and prop-). Numerical modeling of SAXS data was crucial to highlighting a systematic sphere-to-rod micellar transition, otherwise undetected, before the formation of the 2D hexagonal phase in both organo-free and organo-containing systems. Then, two different pathways were found in the formation of the cubic Pm3̅n mesostructure: either an ordering transition from concentrated flocs of spherical micelles (from CTEA+ or CTPA+) for pure TEOS systems or a structural transformation from an intermediate 2D hexagonal mesophase in organosilane systems (from CTA+). Combining the comparison between organo-free and organo-containing systems with numerical modeling, we find that the hexagonal-to-cubic phase transition in the organically modified materials seems to be strongly influenced not only by the obvious presence of the organic group but also by the quicker and more massive condensation kinetics of silicate oligomers on the CTA+ micellar surface. Finally, quite unexpectedly, we find a wormlike-to-sphere micellar transition in the CTPA+ system.