The addition of exogenous organic matter derived from organic wastes has been widely used to restore semiarid, degraded soils, favoring the development of plant cover. After organic amendment, soil particle aggregation can increase due to the increase of organic matter, plant roots and microbially derived compounds. However, the effect of organic amendment addition over time on aggregate formation is not clear. The aim of this work was to study soil particle aggregation of a semiarid, degraded soil 5 years after the addition of a sole dose (120 Mg ha− 1) of non-composted (SS) and composted sewage sludge (cSS). For this purpose, soils were separated into four aggregate-size fractions (8000–2000, 2000–250, 250–53 and < 53 μm) by wet sieving. Macroaggregates were further separated into coarse particulate organic matter (> 250 μm), microaggregrates within macroaggregates (250–53 μm) and silt and clay (< 53 μm). In addition, phospholipid fatty acids (PLFAs) of the treated soils were measured. After 5 years, the amended soils had a higher plant cover and greater amounts of large macroaggregates and microaggregates within macroaggregates than the control soil. Soil organic carbon (OC) was preferentially protected in the microaggregates within macroaggregates of the SS-treated soils, which tended to have higher fungal biomass than the rest of treatments. In contrast, the cSS-treated soils tended to have a lower microbial biomass than the SS-treated soils and showed the greatest relative enrichment of OC in the coarse particulate organic matter occluded in the macroaggregates. These results indicate that, depending on the pretreatment of the sewage sludge, the protection of OC over time occurs in different soil aggregate-size fractions, promoting a higher aggregate-associated OC in the composted amendments as coarse particulate organic matter.