The performance of magnesium-impregnated NaY zeolite catalysts for the glucose isomerisation into fructose at 100 °C has been evaluated. Although crystallinity and textural properties of the zeolites are reduced through Mg addition, glucose conversion improves (6–49%) by increasing magnesium content (0–15 wt.%) due to an increase of the number of basic sites. Conversely, selectivity to fructose drops (96–66%). Nevertheless, good fructose yields were still reached with 10 and 15 wt.% of magnesium (about 32%), being similar or even higher than those found for a commercial hydrotalcite and a pure magnesium oxide. Catalysts lose performance through carbon retention and cations leaching. Deactivation of magnesium-based zeolites was further investigated by consecutive reaction runs. If no regeneration of the catalyst is performed, the activity of the zeolites decreases mainly as a result of cations leaching, the effect reducing with the number of runs. Regeneration allows the catalyst to recover almost totally its initial activity. Interestingly, used samples show higher fructose selectivity due to the additional pore opening resulting from cations leaching and/or carbon removal. Cations leaching results in a homogeneous catalytic reaction which is most significant for the highest magnesium content. Magnesium-based NaY zeolites are revealed as potential catalysts for glucose isomerisation into fructose with high fructose productivities and good performance in consecutive reactions combined with intermediate regeneration.