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This study aims to investigate the effects of inulin and fructooligosaccharides (FOS) supplementation on the viability, storage stability, and in vitro gastrointestinal tolerance of <i>Lactiplantibacillus plantarum</i> in different sugar systems using 24 h growth and 10 days survival studies at 37 °C, inulin, and FOS (0%, 0.5%, 1%, 2%, 3% and 4%) supplementation in 2%, 3%, and 4% glucose, fructose, lactose, and sucrose systems. Based on the highest percentage increase in growth index, sucrose and lactose were more suitable sugar substrates for inulin and FOS supplementation. In survival studies, based on cell viability, inulin supplementation showed a better protective effect than FOS in 3% and 4% sucrose and lactose systems. Four selected sucrose and lactose systems supplemented with inulin and FOS were used in a 12-week storage stability study at 4 °C. Inulin (3%, 4%) and FOS (2%, 4%) supplementation in sucrose and lactose systems greatly enhanced the refrigerated storage stability of <i>L. plantarum</i>. In the gastrointestinal tolerance study, an increase in the bacterial survival rate (%) showed that the supplementation of FOS in lactose and sucrose systems improved the storage viability of <i>L. plantarum.</i> Both inulin and FOS supplementation in sucrose and lactose systems improved the hydrophobicity, auto-aggregation, co-aggregation ability of <i>L. plantarum</i> with <i>Escherichia coli</i> and <i>Enterococcus faecalis</i>.