Several studies have supported the positive functional health effects of both prebiotics and probiotics on gut microbiota. Among these, the selective growth of beneficial bacteria due to the use of prebiotics and bioactive compounds as an energy and carbon source is critical to promote the development of healthy microbiota within the human gut. The present work aimed to assess the fermentability of tomato flour obtained after ohmic (SFOH) and conventional (SFCONV) extraction of phenolic compounds and carotenoids as well as their potential impact upon specific microbiota groups. To accomplish this, the attained bagasse flour was submitted to an in vitro simulation of gastrointestinal digestion before its potential fermentability and impact upon gut microbiota (using an in vitro fecal fermentation model). Different impacts on the probiotic strains studied were observed for SFCONV promoting theB. animalisgrowth, while SFOH promoted theB. longum,probably based on the different carbohydrate profiles of the flours. Overall, the flours used were capable of functioning as a direct substrate to support potential prebiotic growth forBifidus longum. The fecal fermentation model results showed the highest Bacteroidetes growth with SFOH and the highest values ofBacteroideswith SFCONV. A correlation between microorganisms’ growth and short-chain fatty acids was also found. This by-product seems to promote beneficial effects on microbiota flora and could be a potential prebiotic ingredient, although more extensive in vivo trials would be necessary to confirm this.