Crop yields are influenced by multiple, interacting factors, making it challenging to determine how specific management practices and crop rotations affect agroecosystem productivity. This is especially true in cropping systems experiments in which multiple management practices differ between experimental cropping system treatments. We conducted a cropping systems experiment in central Pennsylvania, USA, to analyze the effects of initial cover crop and tillage intensity on feed grain and forage crop productivity during the transition to organic production. We hypothesized that treatment effects of (1) tillage intensity (full or reduced); and (2) initial cover crops (annual rye (Secale cereale) or timothy/clover (Phleum pratense/Trifolium pratense)) on grain crop yield in a 3-year cover crop/soybean (Glycine max)/corn (Zea mays) rotation would be mediated by key agroecosystem function indicators (soil quality, weed pressure, and predatory arthropod activity). We used structural equation modeling (SEM) to attribute yield variation to treatment effects and abiotic factors as mediated by these ecosystem functions. We found that tillage intensity had both direct and indirect effects on corn yields. Full tillage had a direct, positive effect on corn yields, a negative effect on perennial weed density, and negative effect on a soil quality indicator (labile soil carbon). Full tillage also had an indirect effect on corn yields as mediated by perennial weed density. The initial cover crop influenced predatory arthropod activity-density and perennial weeds in year 2 (soybean phase), but had no effects in year 3 (corn phase). Abiotic and site factors influenced crop yields and other ecosystem functions in both rotation years. Our results highlight the utility of analytical approaches that consider the relationships among agroecosystem components. Through the analysis of management effects on multiple ecosystem functions, our results indicate that managing weed populations through tillage in organic systems can have the strongest effect on crop yields, although short-term profit gains may be at the expense of long-term loss in soil quality and beneficial insect conservation.