Digestibility of starch is an essential issue in food science studies due to its close relationship with human health. Most common starchy foods contain rapidly digestible starch, which can lead to chronic diseases, including type II diabetes. Heat-moisture treated potato starch (HPS) followed by inclusion complexation with guest molecules is prepared to improve starch's physicochemical properties, resulting in reduced digestibility. The guest molecules used in this study are linoleic acid (LA), stearic acid (SA), and sodium stearate (SS). The in vitro digestibility of the modified starches over time compared to native starch after gelatinization at 95 °C is examined. The starch complexed with SS results in the least amount of rapidly digestible starch (RDS), followed by LA and SA, consecutively. Furthermore, the starch-SS complexes are the most slowly digestible starch (SDS) and included the highest amount of resistant starch (RS), followed by LA and SA. Sodium stearate results in the highest transformation of RDS to be SDS and RS. Thermal analysis data and microscopy images support the digestion results.