Synbiotics are food supplements that combine probiotics and prebiotics to synergistically elicit a health effect in humans. Lactobacillus plantarum exhibits a remarkable genetic and phenotypic diversity, in particular in strain-specific carbohydrate utilization capacities and several strains are marketed as probiotics. We have screened 77 L. plantarum strains for their capacity to utilize specific prebiotic fibers, revealing variable and strain-specific growth efficiencies on isomalto- and galacto-oligosaccharides. We identified a single strain within the screening panel that was able to effectively utilize inulin and FOS, which did not support efficient growth of the rest of the strains. In our panel tested, we did not find strains that could utilize arabinoxylo-oligosaccharides or sulfated fucoidan. The strain-specific growth phenotype on isomalto-oligosaccharides was further analyzed using high performance anion exchange chromatography and revealed distinct substrate utilization phenotypes within the strain panel. The strain-specific phenotypes could be linked to the strain's genotypes identifying gene clusters encoding for carbohydrate membrane transport systems that are predicted to be involved in the utilization of isomaltose and other (unidentified) oligosaccharides in the isomalto-oligosaccharide substrate. IMPORTANCE Synbiotics combine the concepts of prebiotics and probiotics to synergistically enhance the health benefits associated with these ingredients. Lactobacillus plantarum is encountered as a natural inhabitant of gastrointestinal tract and specific strains are marketed as a probiotic based on their strain-specific health-promoting activities. Strain-specific stimulation of growth through prebiotic substrates could enhance the persistence and/or activity of L. plantarum in situ. Our study establishes a high-throughput screening model for prebiotic substrate utilization by individual strains of bacteria, which can be readily employed for synbiotic match-making approaches that aim to enhance the intestinal delivery of probiotics through strain-specific, selective growth stimulation.