The processing of vegetables generates by‐products that are abundant in polyphenols and antioxidants. However, they degrade rapidly due to poor management and a short life expectancy. The present study aimed to evaluate the effect of in vitro digestion (IVD) on the phenolic compositions, antioxidant properties, and polyphenolic profile of the beetroot pomace (BP), carrot pomace (CP), and tomato pomace (TP) by‐products. The results showed a reduction in phenolic compositions for total phenolic content (TPC), total flavonoid content (TFC), total anthocyanin content (TAC), and total proanthocyanidin content (TPAC), which ranged between 27.55% and 63.34%, 16.38% and 31.43%, 32.58% and 77.41%, and 28.81% and 60.78%, after IVD, respectively. Similarly, antioxidant activity evaluated by 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH), 2,2′‐azino‐bis‐3‐ethylbenzothiazoline‐6‐sulfonic acid (ABTS•+), Ferric‐reducing antioxidant power (FRAP), metal chelating activity (MCA), and reducing power (RP), also showed a reduction. High‐performance liquid chromatography with photodiode array detection (HPLC‐DAD) analysis of individual polyphenols varied widely for free and bound phenolic fractions of samples. Among the polyphenolic fractions, catechin (CAT) and protocatechuic acid (PCA) were the highest in BP and CP, respectively in free forms, has shown to be increased after gastrointestinal digestion. Naringenin (NAR) was recorded with the highest both in their free and bound forms in TP and reduced postdigestion. To the best of our knowledge, the present study is the first report to evaluate the effect of IVD on free and bound individual polyphenolic content in evaluated samples.