Perennial legumes in crop rotations increase soil C sequestration from greater productivity with N₂ fixation. Here, we corroborated increases in soil organic carbon (SOC) and harvests modelled in 5 yr wheat–oats–barley–alfalfa/brome–alfalfa/brome (5Y) vs. 2 yr wheat–fallow (WF) rotations with those measured from 1929 to 2018. Harvest and SOC gains of 100–150 g C m⁻² yr⁻¹ and 15–25 g C m⁻² yr⁻¹ were modelled and measured in 5Y vs. WF rotations with different fertilizer and manure amendments. Modelled gains were closely related to annualized rates of N₂ fixation by alfalfa of 8–10 g N m⁻² yr⁻¹. However, N₂ fixation also drove increases in modelled N₂O emissions of ca. 0.06 g N m⁻² yr⁻¹, which partially offset gains in SOC. Gains in harvest, SOC, and N₂O emissions of 60–90 g C m⁻² yr⁻¹, 15 g C m⁻² yr⁻¹, and 0.05 g N m⁻² yr⁻¹ were modelled and measured in both rotations with amendments of N + P relative to unamended treatments. Harvest and SOC gains were smaller, and leaching and N₂O losses larger, with amendments of N without P. After 100 yr of RCP 8.5 climate change, harvests in WF changed little from those in baseline runs, whereas those in 5Y rose with N + P because of increased N₂ fixation. SOC declined in WF with all amendments and could only be raised in 5Y with N + P amendments. These model findings indicated the importance of N₂ fixation and P amendments in determining responses of agroecosystem productivity and C sequestration to climate change.