The relationship between the productivity of crops of agricultural interest and their interactions with physicochemical soil properties is widely explored. However, there is still a gap concerning the contribution of biological soil attributes and especially the relationship between crop productivity and the structures of organism communities within the soil, such as the enchytraeids. This paper aimed to evaluate the diversity and structures of enchytraeids communities in subtropical soils and their relationship with soybean productivity and soil properties within a no-tillage system. This study was conducted in soybean growing grounds working under no-till farming systems in southern Brazil. Samples were collected according to ISO 23611-3 and extracted with the hot–wet methodology. The organisms were identified up to their genus level. Enchytraeids density increased with the increase of soybean productivity for both evaluated crops. Enchytraeus, Fridericia, and Hemienchytraeus were more abundant in high productivity and genus Achaeta was only found in the second crop and was not a sensitive indicator toward changes in soybean productivity. Regarding the relationship between the enchytraeid community and soil attributes, the variables clay, phosphorus, moisture contents, pH, Ca/Mg as well as carbon and nitrogen from soil and litter, affected Enchytraeidae distribution. Enchytreids showed significant correlations with soybean productivity in the no-tillage system for subtropical soils in Brazil, demonstrating potential bioindicators of soil quality and consequently of soybean productivity.