This work deals with the valorization of fruit industrial processing waste pretreated with two dehydration methods, air oven and lyophilization. Ultrasound-assisted extraction using a sonication probe was selected to recover the high-value fractions. A battery of experiments following a Box–Behnken design was planned to evaluate the effect of the ultrasound amplitude, extraction duration, and temperature on the yield, protein content, phenolic content, and antiradical capacity of the soluble extracts. Operating at a fixed frequency (24 kHz) and solid:water ratio (1:15), the models predicted (significance degree >95%) the maximum extraction conditions of 69.7% amplitude, 53.43 °C, and 12 min for conventionally dehydrated fruit waste. Under these processing conditions, 52.6% extraction yield was achieved, with a protein content of 0.42 mg/g, total phenolic content of 116.42 mg GAE/g, and antioxidant capacity of 44.95 mg Trolox/g. Similar yields (53.95%) and a notably higher protein content (0.69 mg/g), total phenolic content (135.32 mg GAE/g), and antioxidant capacity (49.52 mg Trolox/g) were identified for lyophilized fruit waste. This treatment required a longer dehydration pretreatment duration (double), higher ultrasound amplitude (80%), and higher extraction temperature (70 °C), but shorter extraction time (4 min). These outcomes highlighted the important impact of the dehydration method on the valorization of the tested waste, with conventional drying saving costs, but the lyophilization procedure enhancing the bioactive features of the waste.