Magnesium-impregnated NaY, NaMOR, NaBEA, NaZSM-5 and NaFER zeolites have been prepared and investigated for glucose isomerisation into fructose. It was shown that better magnesium dispersion and smaller reduction of textural properties were obtained with three-dimensional rather than with mono- and two-dimensional zeolites. MgO particle size was also observed to be dependent on the zeolite structure. Various contributions were found to affect the final catalyst performances: availability of MgO, the strength of basic sites, location where the reaction takes place, and the extent of homogeneous reaction due to Na and Mg leaching. Higher glucose conversions were achieved over the MOR, BEA and ZSM-5 zeolites (37–39%), while Y and FER zeolites presented a relatively moderate performance (28 and 27%). In general, lower fructose selectivities were reached for the most active samples, except for the ZSM-5 zeolite. For this catalyst, the reaction appeared to take place mostly on the external surface due to the smaller pore size. Among the various structures investigated, 5%MgNaY zeolite revealed the most resistance to MgO particle size agglomeration during consecutive reaction runs. In addition, 5%MgNaY was found to be the only catalyst capable of recovering its initial activity when regenerated at high temperature. Thus, the type of zeolite structure selected as support for MgO appears to have a significant effect on the catalyst performance for the glucose isomerisation into fructose, with Y zeolite being the most attractive choice for this application.