The proper selection of solvents for biomass upgrading is a crucial task as it should carefully balance the enhancement of reactivity with a facile product recovery. A challenging case is the conversion of glucose and fructose to 5‐hydroxymethylfurfural (HMF). Ionic liquids (ILs) are often employed to boost the activity and selectivity of this process, although the isolation of HMF from the medium remains a major drawback. To investigate such solvent effects in a realistic (dynamic) environment, classical molecular dynamics (MD) simulations of HMF are performed in imidazolium‐based ILs with different anions. Several parameters are identified that directly control HMF–anion interactions, which may hamper product separation, as well as HMF–HMF contacts, which can promote undesired side‐reactions. These computational results would guide future high‐throughput screenings of new and improved IL media.