This study provides a comprehensive analysis of the composition of onion peels, tomato peels, and pistachio green hulls, with a focus on their structural and bioactive compounds. Onion peels, regardless of cultivar, were found to be rich in quercetin and its derivatives, along with other flavonoids and pectin. Tomato peels emerged as a notable source of naringenin (0.52 mg/g in ethanol extract) and rutin (0.24 mg/g in water extract) and showed an unexpectedly high lignin content, comprising nearly 50% of their structural components. Pistachio green hulls demonstrated a high extractive content (63.4 g/100 g), 73% of which were water-soluble. Protocatechuic acid, rutin, and quercetin derivatives were the dominant phenolic compounds in the water extract, while luteolin was most abundant in the ethanol extract. Regarding structural composition, tomato peels and pistachio green hulls shared similarities, exhibiting a high lignin content (53.4% and 33.8%, respectively) and uronic acids (10–15%). In contrast, onion peels were characterized by high levels of glucans (around 38%) and galacturonic acid (33%). The insights from this study pave the way for the design of sustainable and efficient extraction processes, enabling the sequential recovery of valuable bioactive compounds and promoting the valorization of these agro-industrial by-products. Additionally, onion and tomato peels were evaluated as sources of pectin using two extraction methods: conventional acid water extraction and subcritical water extraction. The results revealed significant differences in the pectin composition (53–68% galacturonic acid) and degree of esterification (79–92%) compared to commercial pectin (72.8% galacturonic acid and 68% esterification), highlighting the influence of the raw material and extraction method on the final properties of pectin.
