Freshly harvested goji berry was stored at 4°C or −4°C for up to 21 days to track the evolution of physiological characteristics and nutritional quality after picking. During the 4°C- and −4°C-storage, respiration rates peaked at 205.06 and 131.33 mg (CO2)·kg−1·h−1, respectively, on Day 4, while ethylene production rates peaked at 83.38 and 45.41 µg (C2H4)·kg−1·h−1, respectively, on Day 2. For the −4°C-stored fruit, respiration and C2H4 production rates were significantly downregulated, fruit firmness and marketable fruit rate were well maintained, and accumulations of total soluble solids, polysaccharides, total free amino acids, and total hydrolyzed amino acids were promoted. In contrast, for the 4°C-stored fruit, accumulation of total flavonoids was enhanced, degradation of essential amino acids was delayed, and significantly higher content of zeaxanthin dipalmitate was maintained for most of the storage time. Practical applications As fresh goji is highly perishable, goji is usually marketed and consumed as dried fruit. As a result, there is a lack of information about its postharvest behavior. Our results suggested that fresh goji berry could be stored at 4°C or −4°C for up to 21 days and the fruit could be considered as a climacteric fruit. The presented study provides new insights into the evolution of physiological characteristics and nutritional quality of harvested goji berry stored at different temperatures, and will facilitate the preservation and circulation of fresh goji berry in the supply chain.