Since most conventional methods and solvents so far applied for separation are not efficient or represent environmental and health risks, the food industry and the field of wastewater treatment demand new strategies applicable on an industrial scale that constitute a challenge for the selective and efficient removal or separation of contaminants or compounds of interest, without affecting the sensory and technological properties of the food or generating additional safety problems after treatment. Molecular imprinting technology (MIT) through molecularly imprinted polymers (MIP) with selective target compound recognition and extraction properties as well as tunable green aspects represent a promising alternative for industrial application. This chapter describes aspects associated with its synthesis and directed applications for its potential large-scale use in wastewater treatment and in the food field for the first time.