Abstract Background Fiber-rich feed components possess prebiotic potential to enhance pig health and are considered a potential solution to the high prevalence of post-weaning diarrhea in pig production under the phased suspension of antibiotics and zinc oxide use. Methods We screened the gut microbiota modulatory properties of pectin substrates prepared from sugar beet within the freshly weaned piglet gut microbiome using an in vitro colon model, the CoMiniGut. We focused on testing a variety (13) of sugar beet-derived pectin substrates with defined structures, as well as known prebiotics such as inulin, fructooligosaccharide (FOS) and galactooligosaccharide (GOS), to gain insights on the structure–function related properties of specific substrates on the weaner gut microbial composition as well as shortchain fatty acid production (SCFA). Results Sugar beet-derived pectin and rhamnogalacturonan-I selectively increased the relative abundance of Bacteroidetes, specifically Prevotella copri, Bacteroides ovatus, Bacteroides acidificiens, and an unclassified Bacteroides member. The degree of esterification impacted the relative abundance of these species and the SCFA production during the in vitro fermentations. Modified arabinans derived from sugar beet promoted the growth of Blautia, P. copri, Lachnospiraceae members and Limosilactobacillus mucosae and amongst all oligosaccharides tested yielded the highest amount of total SCFA produced after 24 h of fermentation. Sugar beet-derived substrates yielded higher total SCFA concentrations (especially acetic and propionic acid) relative to the known prebiotics inulin, FOS and GOS. Conclusion Our results indicate that the molecular structures of pectin, that can be prepared form just one plant source (sugar beet) can selectively stimulate different GM members, highlighting the potential of utilizing pectin substrates as targeted GM modulatory ingredients.