This study comprehensively investigates the efficiency of the formulation of tetraethoxysilane (TEOS) and 3-aminopropyltriethoxysilane (APTES) copolymer in sol-gel syntheses as part of a multivariate experiment. A methodology-based response surface was used to estimate the influence of independent variables such as polymerization time and temperature, as well as the ratio of TEOS and APTES components on the surface charge response function and product yield, and in order to predict the best response values. Analysis of variance showed that when assessing the value of the zeta potential, the polymerization temperature and the ratio of components are statistically significant factors, but on the other hand, when assessing the yield of the finished product, only the ratio of components is significant. The combination of various options for temperature, time and ratio of components allows one to obtain a zeta potential in the range from +61.2 mV to -48.8 mV and a product yield of up to 4.7 g. Evaluation of the data with TGA-DTA, FTIR-ATR, and ELS methods showed an unexpected result, according to which the highest degree of polymerization and the highest surface charge were inherent in an amino-deficient system. Thus, the smaller the amino component in the system (the APTES-TEOS molar ratio is 0.25), the more efficient the polycondensation is over the absorption area of the Si-O-Si band, and the higher the zeta potential.