The solid-phase polymerization synthesis (SPPS) represents one of the most innovative approaches to the preparation of nano-sized molecularly imprinted polymers. One of its main features consists of the use of a solid support on which the template molecule is covalently grafted. It implies that the imprinting process does not involve the target molecule as is, but, rather, a structural modification of it. It is known that the rationally designed mimic N-(4-chloro-1-hydroxy-2-naphthoylamido)-(L)-phenylalanine (CHNA-Phe) is able to generate, by bulk polymerization, imprinted materials capable of recognizing the mycotoxin Ochratoxin A (OTA). In this work, we wanted to verify whether the CHNA-Phe can be a useful mimic template in the SPPS technique. The binding isotherm were measured in the pH range of 4–8 and the binding affinities for CHNA-Phe and OTA were compared, showing that CHNA-Phe-imprinted nanoMIPs recognize, in buffered water, equally well OTA, and that the overall molecular recognition depends markedly from pH-related ionic interactions between the ligand and the binding site. There results confirm that in the SPPS method, it is possible and convenient to use as mimic templates a molecule whose three-dimensional structure is to some extent different from the target without substantial loss of selectivity or binding affinity.