This study explored the effect of three different industrial drying methods on the physicochemical, nutritional, and safety profile of goji berries. The hot-air (HD) and microwave drying (MD) methods yielded berries with relatively high polysaccharide content, while vacuum freeze-drying (FD) yielded dried berries with better sensory qualities but relatively less polysaccharide content. The polysaccharides obtained from the HD and MD berries had lower molecular weight, high antioxidant activity and high degrees of Maillard reaction. Further investigations revealed that all three methods, in particular HD and MD, generated high levels of intermediate Maillard reaction products (55.8–86.3 mg/kg) and advanced glycation end-products (fluorescent intensity of 26784–51712), based on significant reduction of reducing sugar and amino acids in the HD and MD berries (p < 0.05). These findings highlight the need to scrutinize the effectiveness of traditional and emerging drying technologies used to produce safe fruits.