5-Ethoxymethylfurfural (EMF), a potential and viable biofuel, was synthesized in one pot from D-fructose by using cheaper and environmentally friendly deep eutectic solvents (DESs) at mild condition. A variety of DESs were synthesized and used under microwave irradiation to get the maximum conversion of fructose and selectivity to EMF. Among various DESs the combination of choline chloride-oxalic acid gave the highest conversion of D-fructose (92%) with yield of EMF (74%) in 3 h at 343 K. A systematic study on effect of different parameters on reaction rate and selectivity was undertaken. Ethyl levulinate (EL) is also formed due to a parallel reaction of D-fructose with ethanol and water generated in-situ coupled with a consecutive reaction of ethanol with EMF. The formation of EL, which is also a fuel additive, was controlled by using lower temperature. DESs are highly reusable and show good activity up to four cycles. All raw materials used in this process are derived from biomass. The process parameters were optimized to get maximum yield of EMF. The process is green.