Abstract Background and Objective: To investigate the efficacy of a new, proprietary high-resistance potato starch as a prebiotic in comparison to inulin and a control. Methods: In this prospective study, an intervention of 9 g of resistant potato starch (RPS, Potatodaat), inulin, or accessible corn starch was given to participants with mild to moderate indigestion for 30 days. Short chain fatty acid (SCFA) levels, changes to the gut microbiome, and changes in clinical symptoms of indigestion were assessed as primary outcomes. Results: Subjects in the RPS (n = 22), inulin (n = 23), and accessible corn starch (n = 22) groups demonstrated similarity in age, sex, and baseline parameters. At 30 days, the groups experienced 21.1%, 6.29%, and 9.15% increases in stool butyrate, respectively. Clinical symptoms like indigestion and flatulence showed greater improvement with the use of RPS compared to the other two groups. Conclusion: Consumption of high resistance potato starch helps improve stool SCFA levels along with clinical symptoms related to digestion, showing its better prebiotic potential as compared to inulin and accessible corn starch. The new high-resistance potato starch can be considered an effective replacement for inulin.