Cover crops can cycle nutrients, enhance soil health, and suppress weeds, thereby reducing the need for inputs and decreasing environmental problems associated with nutrient losses, soil erosion, and non-target herbicide effects. In organic crop production, cover crops are often essential for optimizing cropping system performance. This research aimed to compare three cereal rye (Secale cereale, L.) management strategies for their agronomic, soil health, and economic benefits in organic soybean (Glycine max, L.) production. In 2014-2015 and again in 2015-2016 in central New York, we compared 1) a ‘No cover’ treatment, in which no cover crop was seeded and the soil was moldboard plowed prior to planting soybeans, 2) a ‘Plow down’ treatment, in which cereal rye was terminated with a moldboard plow at jointing stage prior to planting soybeans, 3) a ‘Ryelage’ treatment, in which cereal rye was harvested at boot stage for forage, followed by moldboard plowing prior to planting soybeans, and 4) a ‘Roll down’ treatment, in which cereal rye was roller-crimped, followed by no-till planting soybeans. Soil health analyses showed greater water infiltration and higher soil respiration in the ‘Roll down’ treatment compared to the ‘No cover’ treatment, and greater potentially mineralizable nitrogen (PMN) in the ‘Plow down’ treatment compared to the ‘No cover’ and ‘Ryelage’ treatments in 2016. No significant differences were observed in aggregate stability or active carbon. Weed biomass in soybean was greater in the ‘Roll down’ treatment than in the other three treatments in both years. No significant differences were observed in yield in 2015, but in 2016, yields were lower in the ‘Roll down’ treatment, which was probably due to a combination of extremely dry conditions in June, poor seed-to-soil contact, and reduced soybean growth rate. Economic analysis showed that harvesting cereal rye for ryelage and using tillage prior to growing organic soybean can maximize profitability. Overall, this research shows that cover crops can provide many benefits; however, no one cover crop management strategy provided all benefits and more research is needed to overcome tradeoffs.