Continuous corn (Zea mays L.) silage production, even with no-tillage, can degrade soil quality because of nutrient depletion and minimal organic matter additions. Manure application and the use of different companion or cover crops in corn silage production systems may lessen or prevent soil quality degradation by improving several soil physical, chemical, and biological properties. We quantified the effects of manure, fertilizer, and crop management treatments by measuring extractable P and K, pH, organic C, aggregate stability, bulk density, and microbial biomass and diversity after four years of different manure/cover crop combinations in a no-till production system. Cropping treatments included corn grown with a living mulch of kura clover (Trifolium ambiguum L.) or June-interseeded red clover (Trifolium pratese L.) followed by one year of clover production, and continuous corn grown with June inter-seeded Italian ryegrass (Lolium multiflorum L.), September-seeded winter rye (Secale cereale L.), or no cover crop. Manure was surface-applied annually in April on a P basis. Fertilizer N was applied to the continuous corn treatments above  and to corn grown without manure or cover crop to supply 180 kg/ha available N. There were significant treatment effects on pH, P, K, and bulk density in the surface 0-5-cm soil depth and on large (2-8 mm) macroaggregate stability in all measured soil depths to 30-cm. Effects on overall soil quality were determined using the Soil Management Assessment Framework (SMAF).