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Quinoa (Chenopodium quinoa), a pseudocereal with a complete amino acid profile, offers a promising alternative to wheat, barley and oat in plant-based and gluten-free foods, yet its functional properties and processing side-streams remain underutilised. This study characterised and compared the composition and techno-functional properties of a quinoa protein concentrate (QPC) and its side-stream (SS), produced from a single quinoa flour (QF) fractionation process, to evaluate how processing alters their suitability for food applications. QPC showed markedly higher protein content (39.40 ± 1.60 g·100 g −1 ) than QF (15.28 ± 0.92 g·100 g −1 ) and SS (14.54 ± 0.80 g·100 g −1 ), alongside increased fat (9.20 ± 1.10 g·100 g −1 ) and ash (2.65 ± 0.18 g·100 g −1 ), indicating effective nutritional enrichment. Scanning electron microscopy (SEM) highlighted structural changes induced by processing, supporting observed differences in functionality. Techno-functional analyses revealed that QPC had the lowest emulsion separation rate (0.18%/min, significantly lower than SS p < 0.05) and intermediate protein solubility at pH 7 (26.92 ± 0.83%), water-holding capacity (148.76 ± 0.59%, significantly higher than QF p < 0.05) and oil-holding capacity (63.17 ± 2.99%), positioning it as a suitable protein fortifier for plant-based and gluten-free systems requiring improved emulsion stability and gelation. In parallel, the carbohydrate-rich SS demonstrated potential as a thickening or bulking ingredient, for example in soups, sauces, or other structured foods, supporting more circular use of quinoa processing streams. Overall, this work provides an integrated ingredient and process-level evaluation of quinoa flour fractionation, clarifies the distinct application potentials of QPC and its SS, contributing to the development of sustainable, nutritionally enhanced plant-based and gluten-free food products.