This study examined the effects of different wet-aging times on the physicochemical characteristics and microbial profile of longissimus lumborum (LL) and biceps femoris (BF) muscles from Korean native black goat (KNBG) meat. The water holding capacity (WHC), pH, cooking loss, shear force, meat color, free amino acid, total bacteria, and coliform count of KNGB meat were analyzed at 0, 5, 10, and 15 days of wet-aging at 4°C under vacuum packaging. The results showed that different wet-aging times led to significant pH variations between the muscles throughout the aging period. The wet-aging time did not affect the WHC and cooking loss in meat from the LL muscle. In the BF muscle, however, meat wet-aged for five days had a significantly higher WHC and less cooking loss than meat aged for 0, 10, and 15 days. The meat from the LL muscle wet-aged for five days produced tenderer meat (low shear force value) than the unaged meat (p < 0.05). Moreover, the color was similar in the LL muscle regardless of the number of aging days. In the BF muscle, the redness (a*) was higher in the meat wet-aged for 15 days compared to that aged for 0, 5, and 10 days (p < 0.05). Regardless of the muscles, an increase in wet-aging time led to an increase in the total free amino acids contents in both muscles (p < 0.05). On the other hand, the tasty/bitter amino acid ratio was significantly higher for five days of wet-aged meat than 10 and 15 days of aging from the BF muscle. In addition, regardless of the muscles, the total bacteria and coliform counts were significantly lower for five days of wet-aged meat than 10 and 15 days of aging (p < 0.05). Therefore, chevon wet-aged for five days is an optimal aging period under vacuum packaging that fortifies meat quality with a minimal microbial negative defect.