This paper presents a dynamic principal-agent analysis of an incentive system for Salmonella control in the pork supply chain. The incentive system determines quality premiums to the producer, testing frequencies for hogs delivered, as well as charges to the producer for testing and penalties. Using cost estimates and technical parameters, we evaluate the cost effectiveness of plant and farm control measures and trade-offs between prevalence reduction and related costs and gains. We also assess the impact of ownership structure on incentive system parameters and performance for a wide range of prevalence threshold levels. Differences in control actions, bacteriological prevalence and the overall welfare gain for the chain are very small across ownership structures. Changes in the prevalence threshold level lead to substantial changes in the use of farm and plant control packages and performance measures.