Chemical and physical flaxseed properties can be altered by Brazilian edaphoclimatic and soil management conditions. The study aimed to evaluate the physical and chemical quality of reddish-brown and golden-yellow flaxseeds produced in a conservation management system (i.e., with low agricultural inputs) in Dourados, MS, Midwest region, Brazil. The experiment design was carried out in random blocks, with three repetitions. Significance in difference between two groups were tested by Student t test at 5%. The reddish-brown and golden-yellow flaxseed from Midwest, cultivated under a conservation management system, exhibited similar physical and chemical patterns. However, the reddish-brown flaxseed had a higher hundred seed mass, width, length, color parameters (luminosity, chromaticity, and color angle), neutral detergent fiber contents, phenolic compounds, and stearic and oleic acids than the golden-yellow flaxseed. The flaxseeds produced in the conservationist management system showed the same grain physical and chemical quality as the international and national grains produced in the conventional management system, described in the literature. Our results corroborate the future incentives for increasingly sustainable production while searching for greater eco-efficiency and food security. Thus, the flaxseed cultivated in a conservationist management system has potential to be an economical alternative for all farmers.