The synthesis of mesocellular siliceous foam materials (MCFs) was performed at different stirring rates. In this way, foam samples composed of solid particles differing in size and morphology were obtained. Afterwards, the influence of these physical properties on the adsorptive behavior of the synthesized samples was checked for the adsorption/desorption of an isothiazolone-based commercial biocide (BIO). Results show that at low stirring rates small spheroidal particles were produced. In the absence of stirring, large blocks of silica presenting their external surface fully covered by small homogeneous silica spheres were obtained. Cauliflower-type morphologies were obtained at intermediate stirring rates, while the particle shape became irregular when the stirring rate was increased. On the contrary, the mesostructure and pore size of the particles obtained in the different samples were comparable. The biocide adsorption as well as its subsequent release in aqueous media were strongly affected by the particle size of the silica foam. Adsorption and release tests show that BIO encapsulation in silica foams preserves the biocide structure, obtaining the best performance of controlled release with the matrix synthesized at 400 rpm.