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Conservation practices are increasingly important components of sustainable management systems, and information about their influence on soil characteristics is needed. Soil parameters were assessed in no‐till (NT) or minimum tillage (MT) cotton (Gossypium hirsutum L.) production near Stoneville, MS, Mississippi Delta region, that included cover crop (rye [Secale cereal L.] or Balansa clover [Trifolium michelianum Savi var. balansae (Boiss.) Azn.]) vs. no cover crop. Soils (0–2, 2–5, and 5–15 cm) were sampled (2001–2006) before cotton planting. Independent of tillage, both cover crops accumulated more soil C than no cover, and N was greatest under clover. Soils (0–15 cm) under clover had greater aggregate stability than rye or no cover. The major factor influencing bulk density and infiltration was proximity to crop row bed and wheel traffic, but infiltration rates were sixfold greater under MT than NT (P < 0.01), with less effect of cover crop (P < 0.06, clover > rye or no cover). Moderate tillage slightly increased abundance of both reniform nematodes and earthworms, but neither was affected by cover crop. Fluorescein diacetate hydrolytic activity was higher in clover (50%) and rye (20%) in surface soil than with no cover. Soil microbial community structure (total fatty acid methyl ester analysis) (2005–2006) indicated a significant cover crop effect but no tillage effect. Mycorrhizal bioindicator (16:1 ω5c) was greater in soil with rye than clover or no cover; however, cotton mycorrhizal infection was 40% greater in fibrous roots from rye or clover plots than roots from plots with no cover. Collectively, cotton production with a cover crop and reduced tillage resulted in soil conditions indicative of soil quality.