Commercial Beta, ZSM-5 and mordenite zeolites and commercial montmorillonite K-10 were successfully sulfonated by a one-step simple method using microwaves. Different amounts of the sulfonating agent were required to maximize the incorporation of sulfonic groups for each structure. This has been related to the different dealumination degree suffered by the starting samples during sulfonation together with the different accessibility of the silanols to the sulfonic groups depending on the arrangement and size of their pores. All optimised sulfonated catalysts showed total conversion and very high selectivity (79–91%) to h-GTBE (glycerol di- and tri-ethers), in spite of their microporosity, due to the incorporation of the sulfonic groups that led to a higher number and strength of Brønsted acid sites. Pore size and arrangement together with the external surface area of the catalysts affected the accessibility of the acid sites to the reactants, explaining the evolution of the catalytic results with time for each structure.