This study investigated the effects of geographic region, seed type and processing (soaking and infrared heating) on basic nutrients, anti-nutritional factors, isoflavones and fatty acids in soybean collected in Malawi. Compared with local seed, hybrid seed was significantly (p < 0.05) higher in crude lipids, carbohydrate and sucrose contents but lower in crude protein and stachyose contents. Except for moisture and raffinose contents, soybeans collected from central and north Malawi were not significantly different in contents of all detected components. Infrared heating significantly affected levels of trypsin inhibitors, lectins and isoflavones. Soaking showed significant effects on contents of oligosaccharides, genistin, malonyldaidzin and malonylgenistin. In conclusion, our findings indicated that within central and north Malawi, seed type can lead to more differences among seed components than geographic region. Soaking and infrared heating served as practical approaches to control some anti-nutritional factors while altering levels of the functional components in soybean at the same time.