Quinic acid (QA) and its ester conjugates have been subjected to in-depth scientific investigations for their antioxidant properties. In this study, molecularly imprinted polymers (MIPs) were used for selective extraction of quinic acid (QA) from coffee bean extract. Computational modelling was performed to optimize the process of MIP preparation. Three different functional monomers (allylamine, methacrylic acid (MAA) and 4-vinylpyridine (4-VP)) were tested for imprinting. The ratio of each monomer to template chosen was based on the optimum ratio obtained from computational studies. Equilibrium rebinding studies were conducted and MIP C, which was prepared using 4-VP as functional monomer with template to monomer ratio of 1:5, showed better binding performance than the other prepared MIPs. Accordingly, MIP C was chosen to be applied for selective separation of QA using solid-phase extraction. The selectivity of MIP C towards QA was tested versus its analogues found in coffee (caffeic acid and chlorogenic acid). Molecularly imprinted solid-phase extraction (MISPE) using MIP C as sorbent was then applied for selective extraction of QA from aqueous coffee extract. The applied MISPE was able to retrieve 81.918 ± 3.027% of QA with a significant reduction in the amount of other components in the extract.