The present study aimed to optimize polyphenol extraction from Meghalayan cherry (Prunus nepalensis) pomace using ultrasound-assisted extraction (UAE) and evaluate phenolic profile, antioxidant activity, and bio-accessibility of compounds upon in vitro gastrointestinal digestion. The response surface methodology optimized the process variables (solvent concentration, solvent-solid ratio, extraction time, and amplitude). Under optimized UAE conditions, the yield, TPC, DPPH, and FRAP activity of Meghalayan cherry pomace extracts were 41.25%, 133.88 mgGAE/g, 87.30%, and 0.59 mgAAE/g, respectively. Furthermore, UAE showed higher yield, TPC, and antioxidant activity than conventional solvent extraction (CSE). The percentage bio-accessibility of phenolic acids was higher than flavonoids in both extracts. Hydroxybenzoic acids (113.57% (UAE) and 93.75% (CSE)) showed the highest bio-accessibility in both extracts. In contrast, p-coumaric acid (5.38%) and catechin (26.27%) showed the lowest bio-accessibility in UAE and CSE, respectively. The scanning electron microscope images revealed that ultrasound treatment disrupted the cell wall leading to higher extraction efficiency of polyphenols. Thus, the utilization of Meghalayan cherry pomace can be beneficial for fruit processing industries to manage their waste. UAE was found to be a potential alternative to extract polyphenols from Meghalayan cherry pomace and showed improved bio-accessibility.