The role of the Cr(CO)3 coordination to the aromatic ring of naphtoquinone (NQ) in the polar Diels-Alder (P-DA) reactions with cyclic dienes, cyclopentadiene (Cp), cyclohexadiene (Ch), and 1-methoxy-cyclohexadiene (ChOMe), has been studied within Molecular Electron Density Theory (MEDT). Electron Localization Function (ELF) of the NQ:Cr(CO)3 complex indicates that Cr(CO)3 does not cause any remarkable change in the electronic structure of NQ. While the NQ:Cr(CO)3 complex is categorized as a strong electrophile, the cyclic dienes are categorized as strong nucleophiles, suggesting P-DA reactions. Formation of the NQ:Cr(CO)3 complex reduces the activation energy by only 0.7 kcal·mol−1. While Ch shows a lower reactivity than Cp, ChOMe presents the highest reactivity of this series of cyclic dienes. Analysis of the activation Gibbs free energies of the P-DA reaction with Cp indicates that the reaction is completely endo and anti stereoselective. The present MEDT study shows that the Cr(CO)3 complex has no effective catalytic activity in the P-DA reactions of NQ with cyclic dienes, but only permits the reaction to take place experimentally with a total endo and anti facial stereoselectivity, yielding a single cycloadduct.