European bilberry anthocyanins are promising natural pigments and bioactive compounds, but their application in food systems is limited by their sensitivity to environmental stresses. This study compared apple pectin (AP), citrus pectin (CP), and blueberry pectin (BP) for their effects on the association, stability, and antioxidant activity of bilberry anthocyanins. The optimized complexation conditions were an anthocyanin-to-pectin mass ratio of 1:2.5, pH 3.0, and 80 min. The pectins differed in monosaccharide composition, with (Gal + Ara)/Rha ratios of 2.06, 2.68, and 3.88 for AP, CP, and BP, respectively. Under the these conditions, the binding percentage followed the order AP-A > CP-A > BP-A. FT-IR, XRD, and SEM analyses showed changes in functional group regions, diffraction patterns, and surface morphology after complex formation, consistent with non-covalent association. AP-A showed the highest protective effect among the tested complexes, increasing anthocyanin retention from 48.52% to 64.42% after heating at 90 °C for 5 h and from 8.90% to 37.18% after 5 days of indoor natural light exposure. In the antioxidant assays, AP-A reduced the DPPH and ABTS IC₅₀ values from 46.64 to 31.12 μg/mL and from 0.90 to 0.372 mg/mL, respectively. These findings provide useful information for understanding the relationship between pectin compositional features and anthocyanin stabilization, and may support the rational selection of pectin matrices for anthocyanin-rich food systems.