Weed management is one of the primary challenges for producers transitioning from conventional to organic agriculture. Tillage and the use of cover crops are two weed control tactics available to farmers transitioning to organic management, but little is known about their interactive effects on soil quality during the transition period. We investigated the response of soils to tillage and initial cover crop during the 3-year transition to organic in a cover crop–soybean (Glycine max)–maize (Zea mays) rotation in the Mid-Atlantic region of the USA. The tillage treatment contrasted full, inversion tillage with moldboard plowing (FT) versus reduced tillage with chisel plowing (RT). The cover crop treatment contrasted annual versus mostly perennial species during the first year of the rotation. The experiment was initiated twice (Start 1 and Start 2), in consecutive years in adjacent fields. By the end of the experiment, labile carbon, electrical conductivity, pH and soil moisture were all greater under RT than under FT in both starts. Soil organic matter and several other soil attributes were greater under RT than under FT in Start 1, but not in Start 2, perhaps owing to differences between starts in initial field conditions and realized weather. Soil attributes did not differ between the two cover crop treatments. Combining our soils results with agronomic and economic analyses on these plots suggests that using RT during the organic transition can increase soil quality without compromising yield and profitability.