Nitrogen (N) management is a critical agronomic challenge, as N losses are a source of pollution affecting both waterways and air quality and a potential economic loss for farmers. One approach to N conservation is through ecologically based agricultural systems that reduce tillage and incorporate cover crops. However, these systems exhibit considerable complexity resulting in potential agronomic trade-offs. To address these concerns, four crop management systems were implemented within an organically managed corn–soy–winter grain crop rotation. These systems varied in tillage frequency and intensity, cover crop species selection, cover crop termination and establishment methods, fertilizer management, and cash crop season length. We used field measurements to investigate the impact of each system on N pools and to reveal the strengths and weaknesses of each system in addressing N provisioning services, with a focus on the supply and retention of N before and after the corn phase of the rotation. All systems had greater estimated N inputs (via manure and N-fixation) than outputs (via crop harvest) at the end of the three-year rotation, demonstrating the importance of prioritizing N retention in cover crops. Interactions among system components were important drivers of temporal N dynamics; cover crop species traits and timing of manure application contributed to differences in total aboveground plant biomass N among systems. For example, one cropping system which included a no-till corn planting into a rolled cover crop mulch had soil inorganic N availability that was asynchronous with the N needs of the corn crop even though it received the same amount of N inputs as the other systems. In general, neither interseeding cover crop mixtures nor reducing tillage resulted in marked N benefits at the system level; we did not observe improved N retention from either practice in these systems, and there was no increase in N uptake by corn. What did clearly emerge from this experiment is the importance of managing for synchrony between soil inorganic N availability and cash crop N demand as influenced by the N retention capacity of cover crops and the timing of N mineralization due to tillage.