This study comprises a retrospective analysis of a successful molecular imprint for quercetin with the main aim of deriving rational design strategies for more effective molecularly imprinted polymers. Hence, polymers of varying composition were synthesised and chromatographically characterised to examine the effects of monomer-template ratios. (1)H NMR analysis of the pre-polymerisation mixture yielded further information on the nature of the complexes formed prior to the polymerisation step. A direct correlation between the optimum monomer-template ratio derived from the chromatographic studies and the monomer-template ratio providing the most stable pre-polymerisation complexes observed via (1)H NMR T(1) relaxation time measurements, suggests that the formation of particularly stable pre-polymerisation complexes is responsible for an increased formation of selective binding sites during the polymerisation step. Furthermore, physical aspects of the polymerisation, such as the MIP surface area and macroscopic phase partitioning of the mixture during the polymerisation are investigated. The observed effects and their analytical assessment offer insight into the mechanisms governing MIP selectivity at a molecular level.