The formation process of polyoxometalates [PMo12O40](3-) and [PMo12 - xVxO40](-3-x) has been studied in aqueous solutions of 0.1 M malonate buffer at pH 2.8-3.0 using CZE. Two different approaches, pre-capillary and in-capillary, were examined and compared. In precapillary mode, the reaction mixture of the reactants and reaction products was injected into the capillary followed by the separation procedure. In in-capillary mode, the sequential input of the reagents and running electrolyte into the capillary and the species separation occurs simultaneously. The optimal parameters of in-capillary separation were established as functions of applied voltage and the length of the intermediate buffer zone between the reagents in the capillary. As a result the best-compromise conditions for the separation of the mixtures containing the reactants, intermediates, and reaction products, in order to achieve the best efficiency, symmetry, and peak areas, were achieved at - 18 kV and the input parameter of 900 mbar.s. It was also shown that in-capillary mode is more informative than pre-capillary mode for studying the complex compound formation process.