In this study, proteins were extracted from cress seeds using enzymatic pretreatment and ultrasound. Optimization of enzymatic pretreatment, employing a multi-enzyme complex rich in carbohydrases, aimed to maximize extraction yield and reduce sugar content. Ultrasound replaced classical extraction under optimal conditions by comparing functional properties between enzyme-treated and untreated samples. Combined enzymatic pretreatment and ultrasound significantly increased extraction yield from 39.56% to 94.03%. Optimal enzymatic pretreatment conditions included pH 3.84, 45.16 °C, enzyme concentration 2.32 FBGU/g seed, and 3.71 h of treatment time. Ultrasound-treated isolates exhibited superior functionality and minimal structural changes, with molecular weights ranging from ∼22 kDa to ∼59 kDa. These findings underscore the potential of cress seed protein isolate for diverse applications, enhanced through enzymatic pretreatment and ultrasound, owing to its high nutritional quality.