Zirconium doped mesoporous SBA-15 materials with initial Si/Zr ratios of 10 and 20 have been prepared under microwave-hydrothermal conditions using a non-ionic triblock copolymer surfactant as structure-directing agent, as well as zirconyl chloride and zirconium propoxide as two zirconium sources. The effect of a short (5 min) and long (1.5 h) sol ageing time on the degree of heteroatom incorporation was tested. Changes in the mesopore size and arrangement were monitored with the aid of powder X-ray diffraction (XRD) and gas nitrogen adsorption/desorption at 77 K. The degree of Zr incorporation into the silica framework of the final product was inferred from the analysis by energy-dispersive X-ray spectroscopy and compared with the starting value based on the amount of zirconium added to the reaction mixture. In the case of samples with the lowest initial theoretical molar ratio, the synthesis conditions did not affect the degree of heteroatom incorporation into the silica framework and all zirconium could be introduced under the conditions applied. The structure of materials was strongly dependent on the conditions used, and a more regular pore arrangement was obtained for longer maturation stages. The classical hydrothermal synthesis did not result in a significantly higher efficiency in the heteroatom insertion, though microwave-assisted treatment yielded materials with thicker pore walls. Further increase in the amount of zirconium added to the initial gel did not contribute to a greater heteroatom loading in the final product under microwave conditions.