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Crop systems using cover crops affect soil physical, chemical, and biological attributes, including aggregate formation. This work aims to evaluate winter cover crop species' effect on soil total organic carbon, glomalin, and aggregation in areas with onion crops in a no-tillage vegetable production system (NTVS) and conventional tillage system (CTS) for eight years. The experiment treatments were: control, with natural vegetation(NV); black oats (Avena strigosa); rye(Secale cereale);oilseed radish(Raphanus sativus);intercropped black oats and oilseed radish; intercropped rye and oilseed radish; and a conventional tillage systems area. A 33-year old adjacent secondary forest was evaluated as a reference for undisturbed conditions. We assessed soil total organic carbon, total glomalin, and easily extractable glomalin in three soil layers (0-5, 5-10, and 10-20 cm depth). Undisturbed samples were used to quantify soil aggregate stability, aggregation indexes (weighted mean diameter; geometric mean diameter), aggregate mass distribution (macroaggregates, mesoaggregates), and macroaggregate carbon contents. The conventional tillage areas had the lowest weighted mean soil aggregate diameter, geometric mean diameter, and macroaggregate mass. Those areas also had the lowest bulk soil and aggregate organic carbon contents and the lowest total and easily extractable glomalin. Winter cover crops' use resulted in a 10% higher aggregate weighted mean diameter and geometric mean diameter. Areas with cover crops had 13% higher organic carbon contents in aggregates and 17% higher macroaggregate mass than conventional tillage areas. The highest values of total and easily extracted glomalin occurred in plots with black oats. Winter cover crops, single or intercropped, improved physical attributes of soils with onion crops under not-tillage compared to conventional tillage areas.