Abstract BACKGROUND The agro‐food industry generates by‐products and waste. These may be valorized as protein sources that could be used as alternatives to soy and pea in line with the EU Farm to Fork Strategy. This study evaluated potential safety‐relevant contaminants and the nutritional quality of hazelnut skin protein (HSP) and pumpkin seed protein (PSP) compared with conventional pea protein (PP) and soy protein (SP). RESULTS Microbial contaminants, total aflatoxin, pesticides, and polyaromatic hydrocarbons were assessed as satisfactory. Arsenic, cadmium, and lead slightly exceeded regulatory limits, whereas mercury was undetected. Total protein content was 53.93% in HSP, 57.79% in PSP, 48.86% in PP, and 57.89% in SP. All samples largely met the essential amino acid requirements of the World Health Organization (WHO)/Food and Agriculture Organization of the United Nations (FAO). In vitro cytotoxicity assays showed that HSP and SP significantly affected the viability of colon cancer cells (HCT‐116) while remaining non‐cytotoxic to fibroblast cells (L929), depending on exposure time and protein concentration ( P < 0.05), indicating potentially safe. During in vitro digestion, following the Infogest protocol, HSP exhibited high stability at pH 3.4 with moderate solubility of 20 mg L⁻¹, similar to PSP. Hazelnut skin protein also displayed higher antioxidant activity than SP and PP, reaching 20 mmol TE g⁻¹ after intestinal digestion between 120 and 240 min. CONCLUSION Hazelnut skin and pumpkin seed proteins could serve as alternative protein sources with satisfactory safety and nutritional quality. Further research should focus on safety and nutritional standardization to support their sustainable use as healthy ingredients. © 2025 Society of Chemical Industry.