Reactive oxygen species (ROS) production in disused skeletal muscle induces capillary regression, which disrupts the balance of pro- and anti-angiogenic factors. We tested whether green coffee bean extract containing rich chlorogenic acid, which has antioxidant properties, can prevent capillary regression caused by muscle atrophy. The study included 24 female Sprague-Dawley rats, randomly assigned to four groups: control (CON), 2-week hindlimb unloading (HU), 2-week hindlimb unloading supplemented with coffee extract rich in chlorogenic acids (HU+50%CGA), and 2-week hindlimb unloading supplemented with trace amounts of chlorogenic acids (HU+5%CGA). Rats in the HU+50%CGA and HU+5%CGA groups received an oral dose of coffee extract at 850 mg/kg per day. The effects of chlorogenic acids in coffee extracts were investigated by comparing these groups. Unloading increased oxidative stress, disrupted mitochondrial oxidative activity, and upregulated TSP-1 expression, triggering endothelial cell apoptosis and leading to capillary regression. In contrast, the supplementation with coffee extract containing rich chlorogenic acids prevented ROS overproduction and improved metabolic activity, promoting angiogenesis by correcting the imbalance of pro- and anti-angiogenic factors, and inhibiting endothelial cell apoptosis. In conclusion, green coffee bean extract rich in chlorogenic acids inhibits ROS production, enhances mitochondrial metabolism, mitigates capillary regression by promoting angiogenesis and preventing apoptosis.