Although corn stover is increasingly used as a biofuel, the impact of its removal on agronomic production and soil quality is largely unknown. Cover crops may potentially mitigate untoward effects of crop residue removal. The one year impact of corn stover removal on soil aggregate stability and squash yield was assessed in autumn cover cropping systems. The field experiment consisted of a split-plot design with cover crops (a control with no cover, oat (Avena sativa L.), cereal rye (Secale cereale L.), oilseed radish (Raphanus sativus L. var. oleoferus Metzg. Stokes), and a mixture of oilseed radish and cereal rye) planted at 81, 67, 16, and 9+34 kg ha^-1, respectively, in autumn 2007-2010 as the main plot factor. The retention or removal of corn stover at harvest in autumn 2011 was the split-plot factor, where corn stalks were chopped and either retained on the soil surface or physically removed by hand. A plot composites consisting of three core samples (7.5 cm diameter) at 0-15 cm depth were taken 1 day prior and 30 d later to tillage. Acorn squash (Cucurbita pepo var. pepo) was planted after tillage (May 2012). Wet sieving measurements showed a mean 4.4±1.95% increase in water stable aggregates in stover-retained compared to stover-removed subplots (P=0.0325). Soil aggregation also increased by a mean 5.1±1.93% between monthly sampling times (P=0.0123), however cover crops did not influence soil aggregation (P=0.8591) and there was no stover-by-cover crop interaction (P=0.6419). Stover removal and cover crops did not affect squash fruit yield (P=0.4753) and there was no stover-by-cover crop interaction (P≥0.2103). Although corn stover removal influenced soil quality, there was no impact on subsequent crop yield. Future research will investigate C and N dynamics in these cover crop-corn stover removal systems.