Silica aerogel and lyogel have been successfully sulfonated in one step by a simple post-synthesis method using microwaves as well as conventional heating. The use of microwaves allowed loading higher amounts of sulfonic acid groups in both silicas, according to the higher S/Si atomic ratio determined by XPS, and the higher sulfur content determined by TGA, also exhibiting lower surface area and higher acidity. Sulfonated aerogels showed higher conversion and selectivity to h-GTBE (glycerol di- and tri-ethers) than sulfonated lyogels for the acid-catalyzed etherification of glycerol with isobutene. This was attributed to the higher content of sulfonic acid groups incorporated in aerogel. Microwave-assisted sulfonated aerogel yielded 75% of selectivity to h-GTBE, which can be used as fuel additive, for practically total conversion. Interestingly, larger porosity of aerogel avoided the partial blocking of pores by reaction products observed when other micro- and mesoporous catalysts were tested for this reaction. The combination of high conversion, high selectivity to h-GTBE, practically no formation of undesired di-isobutylenes and very high resistance to catalyst deactivation makes microwave-assisted sulfonic acid functionalized aerogel a promising catalyst for this etherification reaction.