Nationally, the focus on soil quality and function as a foundation for natural resource conservation is rising in importance. The 2002 Farm Bill's Conservation Security Program (CSP) considers soil quality a key component for good land stewardship. The USDA's 2007 farm bill proposal also includes soil quality in several programs. Similarly, the USDA's national organic certification standards also consider soil quality. Yet, it is not clear that the tools and evaluations used to determine program eligibility and certification would yield similar results. To test the assumption that conservation effort is commensurate with resource outcome and that the tools work equally well in conventional and organic farming systems, we compared the results from two program eligibility tools with data from seven organic and conventional farming systems trials across the US. The eligibility tools were the ‘Soil Conditioning Index', a simple, linear predictive model of soil carbon trend, currently used in the CSP, and the ‘Soil Quality Tool', a practice-based index of management effort related to soil function, proposed for use as an eligibility tool. Comparative approaches included t-test and ANOVA of tool outcomes and measured data. We also compared tool outcomes to results from the Soil Management Assessment Framework, a tool for site-specific interpretation of laboratory data that helps to eliminate potential bias in research interpretation. This assessment will be used to help validate and calibrate both tools for future policy implementation.