We present novel data illustrating how soil aggregates control N dynamics and availability for plant uptake by using ¹⁵N-labeled cover crop residue and synthetic fertilizer across conventional and alternative cropping systems.  The experiment was conducted in long-term maize-tomato rotations: conventional (synthetic N only), low-input (reduced synthetic and cover crop-N), and organic (composted manure- and cover crop-N).  Soil and N₂O samples were collected during the maize growing season and the soil samples were separated into three aggregate size classes.  Crop fertilizer-N use efficiency was not different among the three cropping systems.  The majority of synthetic fertilizer-derived ¹⁵N in the conventional system (CMT) was associated with the silt-and-clay fraction, which showed shorter mean residence times (2.6 months) than cover crop-derived ¹⁵N in the silt-and-clay fraction in the organic (OMT) (18.3 months) and low-input (LMT) (14.5 months) systems.  The latter results, plus greater N₂O fluxes and low fertilizer-N recoveries in the soil and crop, suggest that rapid aggregate-N turnover induced greater losses of N and reduced the amount of synthetic fertilizer-N retained in the CMT system.  Also, N-fertilizer type influences SOC and soil N sequestration as the OMT system sequestered 5.7 MgSOCha^-1 and 0.59 MgNha^-1 after 11yrs of continuous organic amendments (~0.47 MgNha^-1yr^-1), whereas SOC and N levels were merely maintained in the CMT system, which received 0.29 MgNha^-1yr^-1 of synthetic fertilizer-N.  In contrast, SOC and N levels declined in the LMT system after the 11yrs of cropping, despite showing intermediate rates of aggregate-N turnover and the highest yield N^-1 applied relative to the CMT and OMT systems.  The application of cover crop-N, alternating with synthetic fertilizer-N, accelerates aggregate-N turnover, thereby, leading to tradeoffs in the LMT system, between the benefits of organic amendments to SOC and N sequestration and N availability for plant uptake versus N susceptibility to loss.