This study describes the changes in the microbial growth, physicochemical properties, phenolics, enzyme activity, and antioxidant activity of Goji berry juice during fermentation with Tibetan kefir grains (TKG). The results showed that TKG grew well in Goji berry juice, and yeasts were dominant in the later period of fermentation (5.20 x 10(8) CFU/mL). The main fungal genus of TKG and fermented Goji berry juice (24, 48, and 72 h) was Kazachstania stably. The relative abundance of Lactobacillus in Goji berry juice decreased from 92.05% to 33.11% after 72 h-fermentation, while that of Acetobacter increased to 66.81%. In addition, 72 h-fermentation led to the consumption of 82.55% of total sugar and 93.90% of reducing sugar, as well as dramatic changes in organic acids. The main volatile substances changed from aldehydes (61.98%) to alcohols (55.24%) and esters (38.54%). The content of total soluble flavonoids (STFC) in Goji berry juice was significantly increased from 42.28 mg RE/100 mL to 85.69 mg RE/100 mL after complete fermentation (p < 0.01). Furthermore, 16 flavonoids, eight phenolic acids, one phenolic acid derivative, and two coumarins were identified by HRLC-ESI-MS/MS. alpha-Amylase and xylanase were primarily responsible for the release of flavonoids (mangiferin, rutin, hyperoside, isoquercitrin, and quercetin) during fermentation, thus significantly enhancing the reducing power and OH. scavenging activity of Goji berry juice.