Sweet chestnuts (Castanea sativa Mill.) are highly prized nuts, and the consumption of fresh chestnuts is usually preceded by roasting, boiling, and frying. The aim of this work was to simultaneously analyze 29 polyphenolic compounds for the first time in raw, boiled, roasted, and fried chestnut seeds and shells using HPLC-MS/MS. Principal component analysis depending on the HPLC-MS/MS results showed that roasting, boiling, and frying affected the contents of 25 detected phenolic compounds in a unique way, of which the most notable phenolics were gallic acid, ellagic acid, and (+)-catechin. Additionally, total polyphenolic content (TPC) was measured via the Folin–Ciocalteu method, and TPC in seeds and inner and outer shells was increased in all treatments except for microwave-roasted seeds. Furthermore, the higher TPC in the inner and outer shells when compared to seeds supported their higher antioxidant activity (AOA) determined via the DPPH experiment. AOA of seeds was increased in all treatments, while the AOA of shells was higher in roasting and lower in boiling and frying treatments. The assessment of these changes is necessary so that chestnut seed consumption and the recycling of their shells as a natural source of antioxidants can be maximized.