Soybean [Glycine max (L.) Merr.] growers using organic production systems have predominately been limited to mechanical cultivation for weed control. Interseeded cover crops such as winter cereal rye (Secale cereale L.) have been used in conventional soybean production systems in conjunction with herbicides to reduce tillage and cultivation operations. The objective of this study was to determine if high soybean planting populations in drill‐planted (19‐cm row) systems or a single mechanical cultivation in row‐planted (76‐cm row) systems could facilitate the use of interseeded rye in organic soybean production systems. Interseeded winter cereal rye decreased soybean grain yield in 2 of 3 yr in the drill‐planted system by 22 and 17%, respectively, and in all 3 yr of the row‐planted system by 23, 27, and 23%, respectively. Moisture stress from the interseeded rye was a predominate factor in soybean grain yield reduction. In 2000, the soybean planting population was inversely correlated with late‐season biomass of interseeded rye. However, during the drier years of 2001 and 2002, increasing soybean planting density did not significantly reduce late‐season biomass of interseeded rye. The interseeded rye reduced late‐season weed biomass in both the drill‐planted and row systems in 2001. Removal of the interseeded rye with mechanical cultivation in the row system when the soybean was at the V4 growth stage was ineffective in 2000 but increased soybean grain yield by 1142 and 746 kg ha−1, respectively, in 2001 and 2002. These results suggest that some means of controlling winter cereal rye growth is necessary for effective management across a range of precipitation levels.