As a result of the increased demand for food, the need to use lower quality water such as saline and waste water in agricultural production increased. The use of saline irrigation water is necessary to provide food for the expected population increases. Salt stress decreases plant growth and yield but negative effects of salt can be reduced by choosing tolerant plants and good agricultural management. Quinoa plants are among the food security plants and are in line with the sustainable development, and are distinguished by their content of unique amino acids and high protein content in their seeds. This study has been conducted to investigate the response of quinoa plant (Chenopodium quinoa Wild) irrigated with saline water to organic amendments. The study was conducted in pots and growth chamber to investigate the response of quinoa to water salinity at the germination and vegetative growth stages. The liner relationship was used to assess the threshold value of water salinity in germination and vegetative growth stages. The study evaluated the effects of eleven salinity levels of irrigation water (0.4, 2, 4, 8, 12, 16, 20, 24, 26, 30, and 34 dsm−1) and organic matter application (farmyard manure) at rats of 20 t ha−1. Quinoa seeds were able to resist the high levels of water salinity in the germination stage, however, the seed germination percentage shows that the increase in irrigation water salinity decreases the final germination percentage. The germination of seeds stopped completely at a salinity level of 26 dsm−1, while at a salinity level of 24 dsm−1 only 50% of the seeds were germinated. Quinoa yield and its components were significantly affected by increasing the salinity level, on the other hand, the addition of organic manure mitigated the salt stress. Quinoa plants lost 50% of the relative yield at water salinity of 18 dsm−1 when no organic amendment was added, while the addition of organic manure increased the threshold value of water salinity up to 34 dsm−1. Adding organic fertilizers to coarse soils increases the ability of quinoa plants to resist saline irrigation water and allows using lower quality water to irrigate these valuable plants. There are many coarse texture soils in arid and semi-arid areas, and improving the level of soil organic matter increases the use of brackish water to irrigate quinoa plants.