A series of zirconium-based metal−organic framework (MOF) nanocrystals (95−211 nm) displaying sulfonate functions (UiO-66-SO3H) was prepared in N,N-dimethylformamide (DMF) - the conventional solvent - and water, and their physicochemical properties were thoroughly investigated. In particular, X-ray diffraction results suggest that upon replacing DMF with water, the resulting MOF crystal structure presents a highly defective structure belonging to the space group Im3̅ instead of typical Fm3̅m. The acid catalysts were applied to the fructose dehydration into 5-hydroxymethylfurfural (5-HMF). Complete conversion of fructose over UiO-66-SO3H prepared in water was reached after only 30 min at 100 °C, in line with its stronger Brønsted acidity. In comparison, its counterpart prepared in DMF showed only 30% fructose conversion. Moreover, the intrinsic catalytic effect at 80 °C was only observed with the water-based UiO66-SO3H. Without reactivation of the catalyst, recycling tests demonstrated the preservation of its structural integrity upon nine consecutive cycles, while a gradual loss of the catalyst activity was attributed to the humin adsorption on the MOFs.