Isoflavones are specialized metabolites found in soybeans seeds. Their distribution in soybean food products are influenced by processing conditions. In this work, soybean seeds (Glycine max (L.) Merrill) variety BRS 257 were roasted and milled to obtain flour known as Kinako. Central composite rotational design (CCRD) was used to analyze the influence of time and temperature on the composition of isoflavones in the Kinako flour. The isoflavones were determined by High-Performance Liquid Chromatography, and the data sets were analyzed by principal component analysis (PCA). The PCA was applied to highlight the relationships between the distributions of isoflavones to the various roasting treatments used to create the flour. High contents of isoflavone-β-glucosides and acetyl-β-glucosides were detected after treatments at 170–200 °C for 11–21 min. High levels of isoflavones aglycones were found after treatment at even higher temperatures and exposure times, thus confirming the conversion of β-glucosides and acetyl-β-glucosides into aglycones. Acetyldaidzin (0.49 mg/g) was majority among acetyl-β-glucosides group and the major aglycones were daidzein, glycitein, and genistein (0.96, 0.83 and 0.41 mg/g respectively). The content of isoflavone found in soy seeds by HPLC combined with chemometrics is able to distinguish different patterns of isoflavones in soy flour produced for food purposes.