Quinoa is a pseudocereal that contains high quality protein, minerals, vitamins, polyphenols, and phytosterols. In this study, quinoa was fermented by Rhizopus oligosporus (R. oligosporus) up to 5 days and the functional compounds (l-carnitine, GABA, vanillic acid and gallic acid) were analyzed by LC/MS. The amounts of l-carnitine and GABA were 0.13 mg/kg and 540 mg/kg for nonfermented quinoa (NF), 3.15 mg/kg and 1040 mg/kg for fermented quinoa at 3 days (3F), and 1.54 mg/kg and 810 mg/kg for fermented quinoa at 5 days (5F). The vanillic acid and gallic acid were 1.3 and 0.1 mg/kg for NF, 1.55 and 2.37 mg/kg for 3F, and 1.83 and 0.84 mg/kg for 5F, respectively. Total phenolic contents and total flavonoids contents were 41 mg gallic acid (GAE)/kg and 13 mg quercetin equivalent (QE)/kg for NF, 74 mg GAE/kg and 16 mg QE/kg for 3F, and 80 mg GAE/kg and 19 mg QE/kg for 5F, respectively. Antioxidant activity (SC50) was 3.6 mg/mL for NF, 3.4 mg/mL for 3F, and 2.3 mg/mL for 5F. Nitric oxide production on RAW264.7 macrophages of fermented quinoa revealed 29% and 56% inhibition of nitric oxide production for NF and 5F, respectively. Therefore, fermented quinoa can be used as a healthy and valuable food product.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0675-3) contains supplementary material, which is available to authorized users.