SummaryGlobal demand for gluten‐free products is rising, however currently most lack protein and are nutritionally insufficient. Tef and fonio, two nutritious gluten‐free cereals might provide a good alternative. To evaluate their composition, a detailed profiling of their free amino acid (AA) and phenolic composition was performed, using UPLC‐QqQ‐MS/MS, in addition TPC and antioxidant activity. Grain morphology was also investigated. Our results reveal the presence of 18 AAs, including all essential, in both tef and fonio. L‐asparagine and L‐tryptophan were the most abundant, whereas cysteine and glutamine were absent. Levels of lysine were sufficient (4.39 and 6.72 mg/g DW for tef and fonio, respectively), but levels of methionine in fonio were low (0.45 mg/g DW). TPC was 0.87 and 0.38 mg GAE/g DW in tef and fonio, respectively. 11 phenolic compounds were identified and quantified in both cereals, ranging from 2,246 μg/g DW to trace levels, with higher levels observed in tef. ABTS Antioxidant activity was 0.25 and 0.15 mg TE/g DW for tef and fonio, respectively, typical for cereals and millets. Overall, our work implies that tef and fonio can make a healthful contribution to human nutrition, and specifically be incorporated into gluten‐free diet to increase protein and polyphenol consumption.