SummaryIn present investigation, the effect of roasting in microwave and oven on bioactive compounds, antioxidant capacity, fatty acid profiles and phenolic constituents of quinoa seeds for free and conjugated phenolic profile fractions are studied. The oil contents of seeds roasted in both roasting systems were recorded between 4.25% (microwave) and 4.80% (oven).Total phenolic amounts of free and bound fractions of quinoa seeds were measured to be between 1668.1 (control) and 2037.5 mg/100 g (microwave) to 638.9 (microwave) to 1615.3 mg/100 g (oven), respectively. Antioxidant activities of free and bound fractions of quinoa seeds were recorded to be between 36.86% (microwave) and 39.28% (oven) to 74.83% (control) and 77.18% (microwave), respectively. Oleic and linoleic acid results of quinoa seed oils roasted in microwave and oven were identified between 17.26% (oven) and 22.41% (control) to 48.39% (oven) and 59.92% (microwave), respectively. 3,4‐Dihydroxybenzoic acid results of raw and roasted quinoa seeds for free and bound fractions were identified to be between 2.84 (microwave) and 4.01 mg/100 g (oven) to 7.43 (oven) and 12.60 mg/100 g (control), respectively. K results of roasted quinoa seeds were recorded between 8701.17 (oven) and 9638.45 (microwave). Results showed some changes depending on roasting systems and fraction types.