This study evaluated the close crop recycling method by using the extract from defective onions. The mixture of the diluted extract (1/500) and nutrients was applied seven times on the onion leaves without spilling it onto the field. The yield and quality of the onions produced by this method (recycle) were compared to those grown organically (control) and conventionally (normal). The yield from the recycling field was increased significantly by 9% compared to that of the control field, while it was decreased by 11% compared to the normal field (p < 0.05). This lower yield was explained by the differences of the mulching vinyl and the fertilizers between the treatments which effect the onion growth during the winter. The content of quercetin in the onions from the recycling filed was increased significantly by 34% and 44% compared to those of the control and normal field, respectively (p < 0.05). It seemed that minerals and biologically active substances in the defective onion extract were effective in increasing the onion growth. In terms of soil microbial biomass, arbuscular mycorrhizal fungi was increased significantly in the recycle field by 40.1% and 30.6% compared to those of the control and normal fields, respectively (p < 0.05). On the other hand, microbial stress (cy19:0/18:1w7c) was decreased in the recycle field by 21.0% and 14.1% compared to those of the control and normal fields, respectively.