The application of herbicides and fungicides (chemical compounds used to control weed and fungal pests, respectively) generally improve peanut yield and grade, however their effect on peanut composition and flavor quality is not well documented. The effects of herbicides or fungicides and their combinations on mineral content, fatty acid composition and flavor quality of Southern Runner peanut were investigated. Fungicide application [chlorothalonil (C) and diniconazole (D)] alone or in combination, improved the yield. Application of most herbicides or fungicides or their combination decreased the long chain saturated fatty acid, eicosenoic acid (20:1), acetone, methyl pyrrole and hexanal content while increasing pyrazine content. Application of imazquin (I) and most of the combinations increased magnesium (Mg) while decreased zinc (Zn) content. Application of benefin (B), metolachor (M), alachlor (A), (B+V), (M+C), and (M+D) increased the oleic linoleic acid (O/L) ratio which should improve the stability of the peanuts. Application of (B+V+A) decreased the flavor intensity of the roasted peanuts. Application of pesticides affected fatty acid composition and flavor quality of Southern Runner peanuts.