A simple and efficient microwave-assisted HNb3O8 catalytic process is proposed for the dehydration of carbohydrates in the aqueous phase. A 5-hydroxymethylfurfural (HMF) yield of 55.9 % was achieved at a high substrate/catalyst weight ratio of 50 from a 10 wt % fructose solution, which is close to the yield achieved by homogeneous aqueous systems. The critical factor for this performance is the fast in situ exfoliation of layered HNb3O8 with the aid of microwave irradiation, which leads to quasi-homogeneous catalytic behavior. Importantly, the catalytic system is also applicable for the one-pot production of HMF from di- and polysaccharides, such as inulin, through a consecutive hydrolysis–dehydration reaction. Additionally, the unique restacking feature of the exfoliated HNb3O8 ensures the good reusability of the catalyst.