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In recent years, interest in the consumption of dried goji berries has increased due to its high bioactive properties. Alternative drying methods that provide faster drying and better preservation of bioactive properties should be developed. This study aims to investigate the effect of different drying methods on the drying time and quality characteristics of the goji berry; namely, hot-air drying (HAD), ultrasound-assisted vacuum drying (USVD), vacuum drying (VD), freeze-drying (FD), and ultrasound-pretreated freeze-drying (USFD). The drying kinetic, total phenolic content, antioxidant capacity, phenolic profile, carotenoid profile, and color change of the goji berry fruit were determined. The drying times for VD, USVD, and HAD varied between 275–1330 min. USVD treatment showed faster drying behavior than the other two drying methods. The total phenolic content (TPC) value of dry samples varied between 1002.53–1238.59 mg GAE/g DM. USVD treatments exhibited a higher total phenolic content (TPC) value than all other drying methods. DPPH and CUPRAC values varied between 15.70–29.90 mg TE/g DM and 40.98–226.09 mg TE/g DM, respectively. The total color change (ΔE) value ranged between 4.59 and 23.93 and HAD dried samples showed the highest ΔE of all samples. The results of the phenolic profile were consistent with TPC analysis. HAD caused higher phenolic compound degradation than VD, USVD, and FD. The results of this study showed that different drying techniques significantly affected the drying rate and retention of bioactive components of the goji berry fruit, and the USVD and VD methods could be used as an alternative to the HAD method. This study concluded that USVD and FD could be considered as suitable drying methods and could be used as alternatives to HAD in the drying of goji berries.