A correlation between polyoxotungstate structures and their catalytic performance for oxidative desulfurization processes was investigated. Bridged lanthanopolyoxometalates that incorporate identical metallic centers with Keggin- EuPW11O3911− and Lindqvist-type Eu(W5O18)29− structures were used as catalysts for the oxidation of the most representative refractory sulfur compounds. Both compounds were able to desulfurize a multicomponent model diesel under sustainable conditions, i.e., using ionic liquid as an extraction solvent and hydrogen peroxide as an oxidant. However, the Lindqvist catalyst appeared to achieve complete desulfurization faster than the Keggin catalyst while using a lesser amount of catalyst and oxidant. Furthermore, the reusable capacity of the Lindqvist-type Eu(W5O18)29− was confirmed for consecutive oxidative desulfurization processes. The contribution of the lanthanide metallic center for the catalytic performance of these compounds was investigated by studying the analogous TB(W5O18)29− compound. Identical desulfurization efficiency was obtained, even reusing this catalyst in consecutive reaction cycles. These results indicate that the active catalytic center of these compounds is probably related to the octahedral tungsten centers. However, a higher number of tungsten centers in the polyoxometalate structure did not result in higher catalytic activity.