MCM-41 mesostructured silicas containing molybdenum and tungsten have been prepared in an acidic medium at room temperature. Two procedures were considered: the so-called oxo–peroxo route with low-nuclearity peroxo metal precursors (route A) and the oxo–polyoxo pathway, involving or generating polyoxometalates (route B). The native materials have been characterised by chemical analysis, powder X-ray diffraction, Raman spectrometry and 29Si MAS NMR. The results show that, in route A, the use of peroxo compounds leads to a distribution of the low-nuclearity metal species throughout the silica-surfactant assembly whereas Keggin type polyoxometalates are generated in route B. The different dispersions of the MOx species (M ¼ Mo, W) on and into the silica matrix and, hence, the formation of MO3 (route B), previously observed for calcined materials, can be explained on the basis of different specific interactions in these organic–inorganic mesophases.