A magnetically recoverable catalyst was conveniently synthesized by the immobilization of sulfonic acid on the surface of silica-encapsulated Fe3O4 nanoparticles, and it was used to catalyze the conversion of fructose-based carbohydrates into 5-ethoxymethylfurfural (EMF). A high EMF yield of 89.3 % was obtained from the etherification of 5-hydroxymethylfurfural at 100 °C for 10 h. The one-pot conversion of fructose could produce EMF with a yield of 72.5 %. More importantly, EMF was also obtained in a satisfactory yield of 63.3 % when the polysaccharide inulin was used as the starting material. The excellent EMF yield showed that the catalyst had strong and sufficient acidic sites, which were responsible for the good catalytic performance. After the reaction, the catalyst could be readily removed from the reaction mixture by means of an external magnetic field, and the catalyst could be reused several times without significant loss in its catalytic activity. Incidentally, the product EMF was easily obtained through the evaporation of the solvent, ethanol, under reduced pressure at low temperature (ca. 40 °C), and the ethanol could also be reused. The integrated utilization of a biorenewable feedstock, magnetically recoverable catalyst, and bio-based green solvent is a typical example of an ideal green chemical process to produce potential liquid fuels.