Soymilk is rich in nutrients and isoflavones, and could greatly promote nutrition and health. However, this product is not widely accepted due to an objectionable beany flavor. Several methods involving heat treatment and soaking in basic solutions prior to soymilk extraction have been reported to reduce the objectionable flavor. However, the effects of such treatments on the nutritional value and isoflavone content of soymilk, and the responses of different soybean varieties to nutrient extraction by these methods is not well studied. The aim of this study was to determine the effect of three processing methods on protein, fat, minerals, and isoflavone content in soymilk from six soybean varieties grown in Rwanda (Peka‐6, SB 24, Sc. Sequel, Sc, Squire, and a local variety) to find the best variety and processing method. The first method (M1) involved soaking soybeans in water for 12 hr prior to milk extraction, M2 involved blanching in NaHCO₃ prior to extraction and M3 involved soaking in NaHCO₃ solution for 16 hr and subsequent cooking prior to extraction. M1 resulted in significantly higher nutrient and isoflavone extraction than M2 and M3. Thus, M1 extracted more nutrients and can be recommended for soymilk production. However, where consumers prefer soymilk obtained by M2 or M3, Sc Squire and the local variety may be recommended. Sc. Squire has another advantage of higher isoflavone content than the other varieties. Further comprehensive studies on the sensory acceptability of products made from different varieties by different methods among different consumer categories will be necessary.