Whole grain insoluble dietary fiber (IDF) is a good source of bound-form polyphenols. In the present study, insoluble dietary fiber rich in bound polyphenols (BP-IDF) from quinoa, rye and wheat was prepared. The carbonyl scavenging capacities of these three BP-IDFs and the effects of in vitro gastrointestinal (GI) digestion and colonic fermentation on their scavenging activities were studied. The results indicated that the fiber-bound polyphenols from quinoa showed the highest carbonyl scavenging capacity compared to those from rye and wheat. After colonic fermentation, more than 73% of the bound polyphenols were still retained in the fermented residues of the quinoa BP-IDF. The fiber-bound polyphenols in the GI-digested residues of quinoa retained considerable carbonyl scavenging activities. During the fermentation process, the residual fiber-bound polyphenols in the fermented residues still scavenged 35.8% to 45.2% of methylglyoxal, 19.3% to 25.4% of glyoxal, 50.7% to 60.5% of acrolein and 5.2% to 9.7% of malondialdehyde, showing a critical role in the scavenging of carbonyl compounds compared to the released and metabolized polyphenols. These findings confirm the capacity of fiber-bound polyphenols from three whole grains to scavenge carbonyls during in vitro digestion and fermentation processes, suggesting that they could be used as functional ingredients to maintain continuous defenses against carbonyls along the digestive tract.