Corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] farmers in the upper Midwest are showing increasing interest in winter cover crops. The effects of winter cover crops on soil quality in this region, however, have not been investigated extensively. The objective of this experiment was to determine the effects of a cereal rye (Secale cereale L.) winter cover crop after more than 9 yr in a corn silage-soybean rotation. Four cereal rye winter cover crop treatments were established in 2001: no cover crop, rye after soybean, rye after silage, and rye after both. Soil organic matter (SOM), particulate organic matter (POM), and potentially mineralizable N (PMN) were measured in 2010 and 2011 for two depth layers (0-5 and 5-10 cm) in both the corn silage and soybean phases of the rotation. In the 0- to 5-cm depth layer, a rye cover crop grown after both main crops had 15% greater SOM, 44% greater POM, and 38% greater PMN than the treatment with no cover crops. In general, the treatments that had a rye cover crop after both crops or after corn silage had a positive effect on the soil quality indicators relative to treatments without a cover crop or a cover crop only after soybean. Apparently, a rye cover crop grown only after soybean did not add enough residues to the soil to cause measureable changes in SOM, POM, or PMN. In general, rye cover crop effects were most pronounced in the top 5 cm of soil.