Anthocyanidins are a class of π-conjugated systems responsible for red, blue, and purple colors of plants. They exhibit the capacity of aggregation in the presence of other natural compounds including flavonols. Such complexations induce color modulation in plants, which is known as copigmentation. It is largely driven by π-interactions existing between pigments and copigments. In this work, the energies of copigmentation–complexation and self-association are systematically evaluated for an anthocyanidin/flavonol couple prototype (3-O-methylcyanidin/quercetin). To describe noncovalent interactions, DFT-D appears mandatory to reach a large accuracy. Due to the chemical complexity of this phenomenon, we also aim at assessing the relevance of both B3P86-D2 and ωB97X-D functionals. The benchmarking has shown that B3P86-D2 possesses enough accuracy when dealing with π–π interactions with respect to both spin component scaled Møller–Plesset second-order perturbation theory post Hartree–Fock method and experimental data. UV–vis absorption properties are then evaluated with time-dependent DFT for the different complexes. The use of range-separated hybrid functionals, such as ωB97X-D, helped to correctly disentangle and interpret the origin of the UV–vis experimental shifts attributed to the subtle copigmentation phenomenon.