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Heteropolyacids (HPA) immobilized onto SBA-15 silica were prepared by two different ways using either impregnation or encapsulation methodologies. Two Keggin-type HPA, H3PW12O40 and H4SiW12O40 were considered in this study. The resulting hybrid materials were fully characterized by N2 adsorption-desorption isotherms, XRD, FT-IR, Raman, diffuse reflectance UV-Vis spectroscopies and 31P MAS NMR. All characterization methods showed that at room temperature the catalysts contained well-dispersed and intact Keggin units throughout the solid. The catalytic activity of these solids was investigated in the isomerization of n-hexane. The impregnated and encapsulated phosphotungstic catalysts performed similarly in catalysis showing that the amount of active sites was nearly the same in both catalysts. On the contrary, the tungstosilicic encapsulated material was completely inactive while its impregnated counterpart was even more active than the phosphotungstic derived catalysts. The acidity of the solids was measured by various methods: microcalorimetry of ammonia adsorption, ammonia desorption followed by Temperature Programmed Desorption (TPD) and DRIFT/GC-MS and pyridine adsorption followed by infrared spectroscopy. Only pyridine adsorption and ammonia desorption followed by DRIFT/GC-MS agreed with the catalytic data. Ammonia adsorption followed by microcalorimetry was not able to differentiate between the four catalysts while the TPD experiments led to unreliable results, as not only the evolved ammonia but also other molecules such as water were taken into account in the measurements. The behavior difference between the encapsulated silico- and phosphotungstic acids was explained by a more pronounced encapsulation in the case of silicon.