Organic flax (Linum usitatissimum L.) was produced on 12,482 ha in the United States in 2005 to meet the demand for organic, food‐grade flaxseed oil. When an organic flaxseed oil facility was established in Iowa in 2004, organic producers requested research information on methods for enhancing soil fertility and weed management in organic flax production. The objectives were to evaluate the effect of compost and red clover (Trifolium pratense L.) underseeding on flax agronomic performance and economic returns under certified organic production management. Flax yields ranged from 1619 kg/ha in 2005 to 940 kg/ha in 2006 and 584 kg/ha in 2007. The underseeding facilitated weed management in 2 of 3 years, when lower grass and broadleaf weeds, respectively, were recorded in underseeded plots in 2005 and in 2007, but yields were lower in red clover plots than in non‐underseeded plots in 2005. In 2 of 3 years, greater yields were obtained with compost applications compared to unfertilized plots, but greater weed biomass and broadleaf weed populations occurred in 1 of 3 years in compost plots. When seed quality was analyzed in 2006, flaxseed oil content averaged 43% across all treatments, which exceeded the market standard of 36%. Economic returns ranged from $747/ha to $632/ha for organic food‐grade and feed‐grade flax, respectively.