Five soymilk quality-related characteristics were investigated as affected by different grinding, heating, extraction methods and varieties. The five characteristics are (1) protein and solid recovery, (2) trypsin inhibitor activity, (3) antioxidant compounds and antioxidant capacity, (4) soy odor, and (5) isoflavone content and profile. The two varieties were Prosoy and black soybeans. The results show that significant differences existed among the three grinding methods (ambient grinding, cold grinding, and hot grinding). Ambient grinding gave the best protein and solid recoveries. Hot grinding showed the best results for the other four parameters. Cold grinding gave the poorest performance, with the exception of the odor profile. The three heating methods (traditional stove cooking, one-phase UHT, two-phase UHT) also resulted in significant differences in the chemical compounds and properties of the soymilk. In many cases, the effects of heating methods were closely related to grinding methods and varieties. Our results clearly demonstrated that a UHT processor equipped with a vacuum chamber was a very efficient way to reduce or eliminate some undesirable soy odors, especially in conjunction with hot grinding. Our results also demonstrated that many complex reactions occurred during thermal treatment. Because of different seed characteristics, the two different varieties behaved differently during processing. For both varieties, extraction with okara washing water from last batch (Method #2) gave the highest solid and protein recoveries.