Soybean and its products became one of the most important functional foods due to its bioactive compounds (isoflavones and bioactive peptides), which have a greet health benefits to human being. In this study, it was prepared a fermented soybean natto with different treatments: drying natto with oven, solar, undervacuum, and extracting them with different solvents to check its antioxidant and antimicrobial activities. Results showed that, acetonitrile extract had the highest amount of peptides followed by methanol extract then water came in the last order. On the other hand, acetonitrile extract had the strongest antioxidant and antimicrobial activities, meanwhile water and methanol extracts had a close effect in general, but still methanol extract had the higher activities than water extract. Methanol extracted all of total isoflavones and some of bioactive peptides, acetonitrile extracted bioactive compounds and some of isoflavones. Upon correlation of these results, it was found that the highest antioxidant and antimicrobial activities excess in acetonitril extract.  Therefore, it was assumed that the antioxidant and antimicrobial activities of natto came from both, isoflavones and bioactive peptides, but bioactive peptides had stronger activities.