Association between anthocyanins and carbohydrates has drawn attention over the past few years and this interaction is of particularly importance in food chemistry since these compounds are often found together in plants and foodstuffs. This work intended to bring insights on the interaction between ionic carbohydrates (pectin) and two anthocyanins (cyanidin-3-O-glucoside, cy3glc and delphinidin-3-O-glucoside, dp3glc). The interaction between the flavylium cation and hemiketal anthocyanin forms was characterized by saturation transfer difference (STD) NMR spectroscopy and the respective dissociation constant (Kd) was obtained. This binding was also studied by Molecular Dynamics simulation. In the presence of the anthocyanin hemiketal form a weak interaction between anthocyanins and pectin seems to occur. A variation in the extent of this interaction was also noticed for the two anthocyanins with dp3glc bearing three hydroxyl groups, revealing to be a stronger binder to pectin (Kd ≈ 180 μM for dp3glc and Kd ≈ 250 μM for cy3glc). Experiments performed at acidic pH (flavylium cation) revealed a much stronger interaction (Kd ≈ 2 μM). These experimental results were also supported by theoretical studies which also revealed a stronger interaction in the presence of the anthocyanin flavylium cation and also a stronger interaction between pectin and dp3glc than with cy3glc (for the hemiketal form).