We developed molecularly imprinted polymers (MIPs) with a poly(ethylene glycol) (PEG)-based cross-linker and boronic acids in functional monomers, which selectively form a complex with a diol structure for selective removal of lactones from a coffee beverage. We synthesized a boronic acid monomer, 1-allylpyridinium-3-boronic acid, which has lower pK(a) and stronger binding strength to saccharides than commonly used boronic acids. Then, we prepared the MIPs with the monomer and succeeded in selective adsorption for a type of lactones, quinic acid gamma-lactone (QAGL). Furthermore, the high hydrophilicity of PEG and the molecular imprinting effect prevented an un-specific adsorption of other components in coffee. Finally, we achieved in removal of QAGL in coffee with high yield and at high speed by using the MIP-based microsphere as a separation medium in solid-phase extraction. This study provides a simple method for better-tasting freshly brewed coffee.