The synthesis of cubic Pm3̄n mesocaged solid templated by cetyltrimethyl ammonium bromide (C16TMABr) surfactant by direct cocondensation of (3-aminopropyl)triefhoxysilanes (APES) under strong alkaline conditions is reported. The novel route gives direct incorporation of amino functional groups on the porous silica wall, and the structural formation has been followed by means of in situ SAXS studies performed at a synchrotron beam line. Data shows that a molar ratio of C16TMABr/APES = 0.6 favors the formation of 3D cubic mesocaged solid with Pm3̄n symmetry which transforms to a cylindrical mesoporous phase with p6mm symmetry at higher molar ratios. Further structural evaluation has been performed by means electron crystallography (EC). Reconstructed 3D models based on EC show the presence of spherical cages (A-cages, 45 Å) and ellipsoidal cages (B-cages, 48 × 43 Å) whereby every cage in the unit cell is connected to 14 nearest cages with a window size of 18 Å. Finally, a mechanism is proposed, denoted S+∼No I-, in which penetration of the neutral aminopropyl moiety within the micellar corona is responsible for the formation of the Pm3̄n phase, accounting for the formation of the hexagonal phase at higher molar ratios and higher temperatures. In comparison to other mesocaged materials with the same symmetry this structure possesses a more open porous network which will help assess its potential in a variety of applications discussed herein.