The microwave process raises considerable interest due to its advantages in the agriculture and food industries. This process has an impact on the chemical components of food. The effect of microwave treatment on the composition of maize flour is not well established. This study aims to determine the primary metabolite (amino acids, sugars, organic acids, etc.) and fatty acid profiles before and after microwave treatment (600 W, 2 min) of maize flour samples using gas chromatography (GC) techniques. Thirty-five different metabolites were identified in all maize flour samples by GC-MS through standard mass spectral libraries. Moreover, ten different fatty acids detected by GC-FID in the samples were confirmed by comparing them with the retention times of the authentic standards. Based on the statistical analyses, it was found that microwave treatment did not result in any significant effect on the general primary metabolite profile and fatty acid composition of the maize flour samples. Both the Hierarchical Cluster Analysis (HCA) and the Principal Component Analysis (PCA) indicated that the data obtained from all samples had good repeatability. The findings from the metabolite analyses provide valuable insights into establishing a background for monitoring and controlling the chemical composition of maize flour when subjected to microwave processing.