Onions are the main dietary source of flavonols that have been associated with important health-promoting properties. Onion treated by high-pressure processing (HPP-treated onion) was subjected to a dynamic gastrointestinal digestion and colon fermentation simulator (DGID-CF) to study the effect on the gut microbiota metabolism in the three colon regions (ascending—AC, transverse—TC, and descending—DC) by means of chronic feeding with 27 g/day for 14 days. HPP-treated onion presented a high content of the flavonols quercetin-3,4’-diglucoside and quercetin-4’-glucoside, and a large percentage of them reached the AC without change. TC and DC progressively increased the total phenolic metabolites 2.5 times respective to day 2, mainly 3-hydroxyphenylacetic, 4-hydroxyphenylacetic, 3-(4-hydroxyphenyl)-propionic, and 3,4-dihydroxyphenylpropionic acids. In addition, the chronic feeding increased the beneficial colon bacteria Bifidobacterium spp. and Lactobacillus spp. and the production of total SCFAs (acetic, propionic, and butyric acids) 9 times (AC), 2.2 times (TC), and 4.4 times (DC) respective to day 1. A multivariate analysis (principal component analysis, PCA) showed a clear separation between the three colon regions based on their phenolic composition (precursors and metabolites). These results showed that HPP-treated onion modulated the human gut microbiota’s metabolism and the DGID-CF is a good system to study these changes.