Microemulsions have been widely used as microreactors for the synthesis of nanoparticles and mesoporous materials. The correlation between the microstructure of a microemulsion and the features of the obtained materials is the most intriguing problem. On this point, many investigations have their ground on the structure of the precursor microemulsion, i.e., the system before the reaction takes place. Nevertheless, any reactions usually involve the formation of byproducts (aside from the nanoparticles). Several of these byproducts (e.g., ions, amphiphilic molecules) could modify the microemulsion structure during the course of the reaction. Here we examine the hydrolysis of tetraethoxysilane (TEOS) in the water-in-oil microemulsion hexadecyl-trimethyl ammonium bromide (CTAB)/pentanol/hexane/water. Conductivity and NMR measurements performed during the course of the reaction, in combination with dynamic light scattering and pulsed field gradient spin-echo NMR investigation performed on the microemulsion upon the addition of ethanol, indicate that a byproduct (ethanol) modifies the microreactor structure. The ethanol produced by the TEOS hydrolysis drives the microemulsion structure from small disconnected reverse micelles toward large connected aggregates until (for high enough ethanol loading) the system phase separates into two coexisting liquid phases (a dense interconnected network and a dilute reverse micellar phase).