Twenty-four cross-breed (Alpine × Beetal) lactating goats (average body weight: 37.5 ± 2.7 kg and milk yield: 1.78 ± 0.31 kg/day) were chosen for the ninety days duration of the experiment and divided into three groups following a completely randomized design. Group I acted as control (T0) and received only a basal diet as per requirement, whereas group II (T1) and group III (T2) received basal diet added with Aloe vera extract at 2% and 4% of dry matter intake (DMI), respectively. Total phenolic compounds (TPC) and milk antioxidant status were higher (p < 0.05) in T1 and T2 than T0. Relative abundance of methanogen, protozoa, Butyrivibrio proteoclasticus, and Ruminococcus flavefaciens in the rumen were lower, while Butyrivibrio fibrisolvens population was higher (p < 0.05) in T2 and T1 compared to T0. Saturated fatty acids levels in milk were lower, whereas different polyunsaturated fatty acids levels were higher (p < 0.05) in T1 and T2 than T0. Nutritional indices of milk increased in both supplemented groups. Overall, it may be concluded that dietary supplementation of Aloe vera extract at 2% and 4% of DMI may enhance the functional characteristics of milk by boosting TPC and antioxidant status, as well as the FA profile and nutritional quality indices of milk fat.