Boot areas in commercial grain elevators and feed mills contribute to commingling of insects with grain that moves through the elevator leg. A partial budget and stochastic dominance model were developed to improve pest management decision-making and risk analysis assessment from commingling effects of insect activity in the boot area. Modified pilot-scale bucket elevator legs, containing residual wheat or corn, were infested with varying insect pest densities prior to clean grain transfers. Appropriate grain discounts were applied to grain samples obtained from clean grain transfers over either: 1) insect-free and untreated boots, 2) infested and untreated boots, or 3) infested and chemicaltreated (β-cyfluthrin) boots. The insect-free boots simulated performing clean-out of the boot area. Partial budget analysis and stochastic dominance modeling indicated that boot sanitation (cleanout) about every 30 d, avoiding costly grain discounts from insect commingling, is the preferred choice. Although chemical spray treatments of the empty boot may reduce insect populations of some boot residual grains, boot cleanout always had lower and usually zero insect pest populations in the boot residual grain, providing higher facility operational net income without the use of chemicals.