With increasing public emphasis on sustainable food production, cover crops (CC) integration into conventional production systems is gaining growers’ interest. However, herbicide residue effects on CC on soil fertility, aggregate stability, and size are poorly understood. In the spring of 2012 and 2013, an untreated check plus pre-emergence (PRE) application of saflufenacil/dimethenamid-p (735 and 1470 g a.i. ha^-1) and s-metolachlor/atrazine mesotrione (2880, 5760, and 140, 280 g a.i. ha^-1) to sweet corn, and imazethapyr (100, 200 g a.i. ha^-1) to pea were set. Post-harvest, rye (Secale cereale L.), hairy vetch (Vicia villosa Roth), oilseed radish (Raphanus sativus L. var. oleiferus), and oat (Avena sativa L.) were planted vertically into herbicide treatments and untreated check. Biomass and N content in CC roots, wet aggregate stability (WAS), aggregate size, and soil mineral N (SMN) in the soil were determined before CC seeding (BCCS) and before main crop seeding (BMCS). Root biomass in vetch and radish was reduced by imazethapyr and 2× rates of saflufenacil/dimethenamid-p and s-metolachlor/atrazine mesotrione. Greater aggregate size in winterkilled CC (oat, radish) plots and WAS in oat-plots was likely due to availability of decomposable residues. SMN was unaffected by CC root N content. This preliminary study demonstrates herbicide residue effects on CC reduction and potential impact on soil quality parameters.