Hot water is an easily implementable process for polyphenols extraction. To evaluate the effect of this process on apple pomace, the overall polyphenolic composition was assessed before and after hot water extraction, followed by extractions with aqueous/organic solutions. As determined by UHPLC-DAD, flavan-3-ols were the main apple native polyphenols. Their amount decreased 50% after hot water extraction, while the other classes remained unchanged. Dihydrochalcones and hydroxycinnamic acid oxidation products, were also observed, alongside with non-extractable oxidised procyanidins that represented more than 4-fold the amount of native apple polyphenols in the pomace. Microwave superheated-water extraction of the insoluble cell wall material in water/acetone solutions and the high amounts of polyphenols that were insoluble in water/ethanol solutions suggested that oxidised procyanidins could be covalently linked to polysaccharides. These complexes represented up to 40% of the available polyphenols from apple pomace, potentially relevant for agro-food waste valuation.