Soybean isoflavone (SIF) in soybeans are natural phytoestrogens, which is functioned as an estrogen agonistic or antagonistic. SIF regulates the capacity of animals to synthesize triacylglycerols by directly utilizing long-chain fatty acids. However, few studies have focused on its regulatory lipid metabolism in lactating dairy goats. The objective of this study was to investigate the influence of SIF on milk yield and composition using Saanen dairy goats as a model, employing both in vivo and in vitro approaches. In the in vivo phase, a total of 20 goats were randomly divided into two groups: the control group fed a basal diet, and the experimental group fed a basal diet supplemented with SIF at a dosage of 100 mg per day. The results underscored a significant elevation in serum estrogen and prolactin levels in the SIF-supplemented group (P < 0.05). Notably, SIF supplementation also displayed a higher milk fat percentage (P = 0.03). Transitioning to in vitro experimentation, the addition of SIF (75 μM) to goat mammary epithelial cells (GMECs) exhibited a pronounced effect on cell proliferation. It spurred cell proliferation and led to an increase in triacylglycerol levels (P < 0.05). Consistently, SIF showcased an enhancement in the expression of key genes associated with milk fat de novo synthesis. SIF demonstrated a rescuing effect on the suppressive impact of MK2206 on Akt protein phosphorylation. Importantly, the study observed that the knockdown of estrogen receptor alpha (ERα) expression completely counteracted the effect of SIF on lipid droplet accumulation. Collectively, the current study establishes the critical role of SIF in process of fatty acid de novo in the goat mammary gland. This regulation is notably mediated through the ERα-Akt axis, thus enriching our understanding of this intricate biological process. This research sheds light on the potential benefits of SIF supplementation in dairy goat farming, ultimately contributing to improved milk production and quality.