Presently disclosed are methods and apparatus for separation of reaction products from reaction mixtures in an ionic liquid catalysis process, particularly in conversion of biomass, cellulose, and sugars into chemical intermediates such as 5-hydroxymethylfurfural (HMF). In one embodiment an ion exclusion adsorption mechanism is used for the separation process. The process comprises (i) mixing the ionic liquid-containing reaction mixture with de-ionized water, (ii) flowing the water solution mixture into an adsorption column, (iii) eluting the column with a water- and/or alcohol-based fluid, and (iv) collecting separated fractions at different elution times.