Corn (Zea mays L.) stover is a potential bioenergy feedstock, but little is known about the impacts of reducing stover return on yield and soil quality in the Northern US Corn Belt. Our study objectives were to measure the impact of three stover return rates (Full (~7.8 Mg ha−1 yr−1), Moderate (~3.8 Mg ha−1 yr−1) or Low (~1.5 Mg ha yr−1) Return) on corn and soybean (Glycine max. L [Merr.]) yields and on soil dynamic properties on a chisel-tilled (Chisel) field, and well- (NT1995) or newly- (NT2005) established no-till managed fields. Stover return rate did not affect corn and soybean yields except under NT1995 where Low Return (2.88 Mg ha−1) reduced yields compared with Full and Moderate Return (3.13 Mg ha−1). In NT1995 at 0–5 cm depth, particulate organic matter in Full Return and Moderate Return (14.3 g kg−1) exceeded Low Return (11.3 g kg−1). In NT2005, acid phosphatase activity was reduced about 20% in Low Return compared to Full Return. Also the Low Return had an increase in erodible-sized dry aggregates at the soil surface compared to Full Return. Three or fewer cycles of stover treatments revealed little evidence for short-term impacts on crop yield, but detected subtle soil changes that indicate repeated harvests may have negative consequences if stover removed.