Metabolomics is a method with considerable unexploited potential in functional genomics, capable of identifying genetic and physiological differences in plants. Therefore, comprehending the metabolic differences of cassava genotypes is crucial for enhancing the traits favoured by farmers and consumers among other factors. We employed a liquid chromatography—mass spectrometry quadrupole (LC-MS qTOF) to examine the metabolic profiles of four cassava genotypes under controlled conditions and discovered 3,372 metabolite features. Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) revealed significant differences in metabolic patterns between genotypes. P4/10 showed the most substantial split, while UKF4 showed only little divergence. Furthermore, the results indicated that lipids, polyphenols, organic acids, and flavonoids were the key metabolites responsible for genotype separation. A pathway analysis indicated significant contributions from the phenylpropanoid biosynthesis, fatty acid degradation, and flavonoid biosynthesis pathways, highlighting the importance of genotype-specific metabolic profiles in determining cassava's biochemical diversity. These findings underscore the significance of metabolic blueprints in defining distinct characteristics among genotypes. Moreover, subsequent research may investigate the genetic foundation of metabolic diversity and its potential to develop enhanced cassava genotypes with superior nutritional value and stress resilience.