Long-term application of organic amendments combined with inorganic fertilizers improves soil aggregation and carbon storage compared to inorganic fertilizers alone. Soil aggregation is measured by aggregate indices like mean weight diameter and water stable aggregates. More carbon is stored in macroaggregates than microaggregates, and application of organic amendments increases carbon stored in both aggregate fractions and total soil carbon. The combination of organic and inorganic inputs provides the greatest benefits to soil structure and carbon storage over long-term use.