According to the EU’s organic regulation, the use of organic seed is generally binding in organic farming. Because of an organic seed shortage, derogations to use nonorganic seed can be obtained. By 2036, the EU plans to phase out these derogations and achieve 100% organic seed use. Previous attempts at achieving this, though, have failed. Ensuring organic seed supply is of particular EU-wide importance to meet EU policy goals, such as the farm-to-fork strategy. To assess the impact of measures to smooth this transition, we developed the VAL-MAS model (VALue chain Multi-Agent System). VAL-MAS is a multiagent model based on a heterogeneous agent population and mathematical programming that can provide insights into the performance of different seed system interventions. We selected organic fresh market carrots in Germany for their importance in the national and European organic sector as an example case. Our model suggests that the end of the derogation system poses a challenge to the seed value chain in terms of seed supply and farm incomes. The most effective mitigation solution is an investment in improved pest control during seed multiplication, accompanied by a stepwise phasing out of derogations for the use of nonorganic seed.