Cell wall polysaccharides (CWPs) and phenolic substances, e.g., procyanidins, widely co-exist in fruit and vegetables and interact in complex patterns during chewing, food processing and in vivo digestion, impacting the food physicochemical and nutritional qualities. Interactions were characterized between two procyanidins and heterogeneous CWPs (four native and twelve modified) from apple, beet and kiwifruit presenting various chemical compositions and physical structures. ATR-FTIR discriminated the complexes from the initial purified procyanidins and CWPs. Langmuir isotherms and ITC indicated that native CWPs, from all botanical origins, had a higher affinity for procyanidins than the modified ones, which were all poorer in pectins. The CWPs thatinteract more with procyanidins were characterized by their high pectin content and linearity, and high porosity. Increasing the molecular size of procyanidins increased their complexation with CWPs. This work is an important guide to the encapsulation and controlled release of active compounds and the subsequent respective digestive behavior and human health.