The development of new methods for the rapid, sensitive, and selective detection of SARS-CoV-2 is a key factor in overcoming the global pandemic that we have been facing for over a year. In this work, we focused on the preparation of magnetic molecularly imprinted polymers (MMIPs) based on the self-polymerization of dopamine at the surface of magnetic nanoparticles (MNPs). Instead of using the whole SARS-CoV-2 virion as a template, a peptide of the viral spike protein, which is present at the viral surface, was innovatively used for the imprinting step. Thus, problems associated with the infectious nature of the virus along with its potential instability when used as a template and under the polymerization conditions were avoided. Dopamine was selected as a functional monomer following a rational computational screening approach that revealed not only a high binding energy of the dopamine-peptide complex but also multi-point interactions across the entire peptide template surface as opposed to other monomers with similar binding affinity. Moreover, variables affecting the imprinting efficiency including polymerization time and amount of peptide and dopamine were experimentally evaluated. Finally, the selectivity of the prepared MMIPs vs. other peptide sequences (i.e., from Zika virus) was evaluated, demonstrating that the developed MMIPs were only specific for the target SARS-CoV-2 peptide.