Mulberry is rich in bioactive substances, which might undergo biotransformation through microbial fermentation, and therefore show great prospect in improving the bioavailability of these substances. We studied the differential metabolites in mulberry juices fermented by Pichia kudriavzevii S1 and Weissella confusa L1 alone or in combination. The sensory analysis using electronic nose and electronic tongue showed that fermentation caused higher response value of aromatic components, reduced bitterness and bitter aftertaste of the juices. The differential metabolites of juices identified by non-targeted metabolomics showed that the contents of total anthocyanins, total flavonoids and total polyphenols in juices fermented by W. confusa and P. kudriavzevii increased by 13.34%, 43.75% and 9.40%, respectively. A total of 10 categories involving 111 kinds of key metabolites were identified in four different treatment groups. These metabolites were mostly involved in amino acid, flavonoid and anthocyanin metabolism pathways. This study might offer new pathways for improving the functional features of mulberry juices through microbial fermentation.