Cotton (Gossypium hirsutum L.) production is heavily reliant on herbicides, but manipulation of soil plant residues under conservation management practices may facilitate sustainable weed control. In no-tillage (NT) or reduced tillage (RT) cotton production, the effects of cover crops [rye (Secale cereale) or balansa clover (Trifolium michelianum ssp. balansae)] and no cover crops on various soil quality parameters were compared. Soils were sampled in late spring 2005 and 2006 after cotton emergence. Cotton roots were harvested (25 roots plot^-1) in 2006, rinsed, and stained for determination of mycorrhizal infection. Both rye and clover NT surface (0 to 2 cm) soils, had the highest organic C, and soils under NT clover had the highest total N. There was no effect of tillage on fluorescein diacetate (FDA) hydrolytic activity; however, both clover and rye had approximately 50% and 20% higher FDA activity in the surface 0 to 2 cm and 2- 5 cm soil, respectively, compared to no cover crop soil. Soil microbial community structure was assessed based on total fatty acid methyl ester (FAME) analysis. FAME analysis of soils collected at planting in 2005 and 2006 indicated a significant effect of cover crops, but not tillage. Both years, the mycorrhizal bioindicator (FAME 16:1w5c) was greater in soil from rye plots compared to clover or no cover crop. Mycorrhizal infection on cotton fibrous roots collected from rye or clover plots in 2006 had at least 40% greater density of mycorrhizal infection compared to roots from no cover crop plots (0.72, 0.62, and 0.39 infections cm^-1 for rye, clover, and no cover crop, respectively). Cotton yields often have been higher under rye cover crop in this ongoing study (initiated 2000), and the stimulatory effects of rye on mycorrhizal infection in cotton roots might be a contributing factor.