Doenjang, a fermented soybean paste, is a traditional food ingredient in Korea. While the flavor of doenjang is heavily dependent on koji, studies on the aroma characteristics of koji remain limited. This study aimed to determine the changes in the aroma profiles of soybean koji (SBK), rice koji (RK), and wheat koji (WK). Aroma analysis was performed using stir bar sorptive extraction followed by gas chromatography‐mass spectrometry (GC‐MS) and descriptive sensory analysis. In SBK, bean‐associated aroma was strongly developed due to the lipid‐derived compounds, whereas in RK, sweet aromas were relatively strong at 72 h due to the sweet‐smelling ester compounds. In WK, the nutty cracker attribute was significantly strengthened during fermentation due to the high concentration of aldehydes. The results showed that the aroma profile of koji was influenced by main ingredient, and this finding is useful in improving aroma development with the use of koji in the fermented food industry. Practical Application Koji is one of the key ingredients utilized in commercialized doenjang making process in Korea, in order to accelerate the fermentation process. In this study, influences of raw materials of koji in the aroma development of doenjang were investigated using descriptive sensory analysis and instrumental flavor analysis using GC‐MS. Raw material‐driven aroma compounds were documented in different koji samples, in which influences the aroma characteristics of doenjang made with koji made with different raw materials. Finding from this study can aid doenjang manufacturers for versatile aroma development of commercialized doenjang.