Quinoa (Chenopodium quinoa Willd.) has recently gained more interest due to its high nutritional value such as high protein quality, high phenolic and dietary fiber contents. However, saponins present in quinoa negatively impact its nutritional and sensory attributes. The aim of this study was to investigate the effects of washing process, which is commonly used to eliminate the undesired effects of saponins, on phenolic and saponin contents, and antioxidant capacities of different colored quinoa seeds. Our results show that red (55.02 mg GAE/100 g) and black (53.25 mg GAE/100 g) quinoa seeds had significantly higher total phenolic contents than their white (46.27 mg GAE/100 g) counterparts (p<0.05). Generally, red quinoa exhibited higher antioxidant capacity, compared to black and white seeds. The washing step caused a significant reduction in phenolic contents and antioxidant activities of all quinoa types (p<0.05), while the reduction in saponin contents was insignificant (p>0.05). Moreover, the disc diffusion assay indicated that quinoa seeds have no inhibitory activity against the tested bacteria. Consequently, red and black colored quinoa seeds have better functional properties than white counterparts. Herewith, development of improved washing methods for more efficient removal of saponin from quinoa seeds while protecting its bioactive compounds is advised.