Awareness towards utilizing food-processing by-products are increasing in health as well as environmental purview. Coffee silver skin (CSS), potato peel (PP) and brewer’s spent grain (BSG) are voluminous by-products in their respective processing industries. The present study compared these three by-products for their prospective utilization in producing polyphenols-rich aqueous extracts by using ultrasound-assisted extractions (UAE). A probe-type sonicator was used for ultrasound treatments. The total phenolic contents in the extracts were assessed by Folin-Ciocalteu assay, while the phenolic profiles of the extract was characterized by LC-Q-TOF mass spectrometry. The microstructure of the samples after UAE was evaluated by scanning electron microscopy (SEM). Ultrasound treatment enhanced the rate of extraction and recovered 2.79, 2.12 and 0.66 mg gallic acid equivalents/g of TPC from CSS, PP and BSG, respectively in 30 min, which correspond to recoveries of 97.6%, 84.5% and 84.6%, respectively, compared to conventional solid–liquid extractions carried out for 24 h. The extraction yield was dependent on the particle size of the raw materials and the highest yield was obtained from the materials with 100–250 µm particle size. The SEM imaging revealed that ultrasound treatment caused prominent tissue damage. Extracts contained mainly hydroxycinnamic acid derivatives of phenolic acids. PP and CSS had the highest amounts of umami free amino acids (0.13 mg/g in each), while BSG contained the highest amount of essential amino acids (92 mg/g). The present work shows that CSS, PP and BSG are good sources of polyphenols and UAE can be employed to enhance the extraction efficiency as means of a green approach.