This study sought to extract phenolic compounds (PC) from the byproduct peels of starfruit (AC-p), camu camu (MD-p), and elderberry (SP-p) through laboratory-scale ultrasound-assisted extraction (UAE). The UAE process used different levels of acoustic energy density (AED = 25–100 J/mL) and nominal amplitude. The particle size and distribution AC-p, MD-p, and SP-p were characterized. The total phenolic content (TPC) extracted via small-scale laboratory UAE using an S24d7 sonotrode (UAE-S24d7) exhibited no significant variation at amplitudes of 49 and 63 µm, achieving a maximum value at 25 J/mL, as confirmed by Fourier-transform infrared (FT-IR) spectroscopy. The TPC and AED for UAE-S24d7 were modeled using a diffusion-based mathematical approach, and the ultrasonic net power of UAE was observed in the order of AC-p > MD-p > SP-p, which correlates with particle size distribution and temperature increase, as confirmed by thermal analysis. The TPC of extracts obtained through laboratory-scale UAE (25 J/mL and 49 µm) using an S24d14 sonotrode (UAE-S24d14) did not differ statistically from those obtained using an S24d7 sonotrode (UAE-S24d7). The PC were identified using liquid chromatography tandem mass spectrometry in AC-p, MD-p, and SP-p at UAE-S24d14, including flavonols, proanthocyanidins, hydroxycinnamic acids, anthocyanins, flavan-3-ols, flavone, and hydroxybenzoic acid derivatives. The laboratory scale-up extracts also demonstrated antioxidant capacity, assessed by DPPH (138.1-307.6 μmol TE/g), ABTS (154.2-466.7 μmol TE/g), ORAC (483.1-882.9 μmol TE/g), and superoxide anion (413.2-4964.62 μmol TE/g). In conclusion, AED and nominal amplitude facilitate the laboratory scaling-up of UAE for the valorization of food by-products.