This study investigated the impact of microwave treatment on the formation of starch-lipid complexes, and physicochemical properties of wheat starch (WS) fortified with lipids, such as lauric acid (LA), glycerol monolaurate (GML), and stearic acid (SA). Specimens were prepared using a conventional water bath and microwave heating and evaluated using macrostructural and microstructural analyses. Iodine staining and scanning electron microscopy revealed interplay between WS and LA. Diffraction peaks around 7.5°, 13°, and 20° and the absence of the absorption band in the 2850 cm−1 were observed in microwave treated WS-lipid samples than conventional water bath samples. Further, more type I complexes were formed in WS-LA microwave-assisted samples, as demonstrated by differential scanning calorimetry. Additionally, more resistant starch was formed in specimens treated by microwave than water bath treated counterparts, the finding that was proved by in vitro enzymatic hydrolysis. In short, the current study may suggest the applications of microwave treatment in foods for hypoglycemia.