Fructosazine and 2,5-deoxyfructosazine are two natural chemicals with various applications as flavoring agents in food and tobacco industry; the 2,5-deoxyfructosazine has also anti-diabetic and anti-inflammatory activities. In order to quantify these compounds in natural samples such as plant or food, we have developed a selective technique based on a water-compatible molecularly imprinted polymer (MIP). MIPs are prepared with a covalent approach from 2,5-deoxyfructosazine as template formed in situ by the self-condensation of glucosamine with vinylphenyl boronic acid, taken as catalyst and covalent monomer during the pre-complexation step. Acrylamide and polyethylene glycol diacrylate are used as supplementary non-covalent functional monomer and cross-linker, respectively. For the first time, a highly cross-linked but highly polar imprinted polymer of fructosazine and deoxyfructosazine is obtained as a solid material and not a gel. Amount of monomers is optimized to obtain high selectivity for both molecules. Results show that the MIPs prepared have a significant imprinting effect with a resulting imprinting factor of 3 for both templates. Molecularly imprinted solid-phase extraction is then performed and could be used in routine analysis to extract 2,5-deoxyfructosazine and fructosazine from soy sauce.