The aim of this study was to investigate the changes produced in the nanostructures and the photoluminescence spectra of bridged silsesquioxanes containing urea or urethane groups, by varying the relative rates between the self-assembly of organic domains and the inorganic polycondensation. Precursors of the bridged silsesquioxanes were 4,4'-[1,3-phenylenebis(1-methylethylidene)] bis( aniline) and 4,4'- isopropylidenediphenol,end-capped with 3-isocyanatopropyltriethoxysilane. The inorganic polycondensation was produced using either high or low formic acid concentrations, leading to transparent films with different nanostructures as revealed by FTIR, SAXS, and Si-29 NMR spectra. For the bridged silsesquioxanes containing urea groups the self-assembly of organic domains was much faster than the inorganic polycondensation for both formic acid concentrations. However, the arrangement was more regular and the short-range order higher when the rate of inorganic polycondensation was lower. The photoluminescence spectra of the most ordered structures revealed the presence of two main processes: radiative recombinations in inorganic clusters and photoinduced proton-transfer generating NH2+ and N-defects and their subsequent radiative recombination. In the less-ordered urea-bridged silsesquioxanes a third process was present assigned to a photoinduced proton transfer in H-bonds exhibiting a broad range of strengths. For urethane-bridged silsesquioxanes the driving force for the self-assembly of organic bridges was lower than for urea-bridged silsesquioxanes. When the synthesis was performed with a high formic acid concentration, self-assembled structures were not produced. Instead, large inorganic domains composed of small inorganic clusters were generated. Self-assembly of organic domains took place only when employing low polycondensation rates. For both materials the photoluminescence was mainly due to radiative processes within inorganic clusters and varied significantly with their state of aggregation.