Sorghum milling waste stream (bran), contains diverse phenolic compounds with bioactive properties. The study determined the potential of microwave assisted extraction (MAE) to recover the bran phenolic compounds. Red, white, and lemon-yellow pericarp sorghum brans were subjected to MAE and phenolic yield and structural transformation vs conventional extraction (control) assessed by UPLC-MS/MS, Folin-Ciocalteu and Trolox equivalent antioxidant capacity methods. Phenols yield increased from 3.7-20.3 to 12.6-75.5 mg/g, while antioxidants capacity increased average 3.3X in MAE extracts vs controls. Hydroxycinnamic acids increased most dramatically (3.0-32X) in MAE extracts (0.08-2.64 to 2.57-8.01 mg/g), largely driven by release of cell-wall derived feruloyl- and coumaroyl-arabinose. MAE hydrolyzed flavonoid glycosides into aglycones, and depolymerized condensed flavonoid heteropolymers into flavanones, flavanols and (deoxy)anthocyanidins. Thus, MAE dramatically enhances yield of valuable phenolics from sorghum bran waste, but also alters the phenolic profile in ways that may influence their chemical and biological properties.