Despite the potential to provide N to crops, the rapid incorporation of green manure nutrients into stable fractions of organic matter in the soil (SOM) may reduce the efficiency of green manuring. Thus, the objective of this work was to characterize the changes of C and N stocks in fractions of SOM cultivated with coffee (Coffea arabica L.) and fertilized with sunn hemp (Crotalaria juncea) and ammonium sulfate. To study the changes in organic C (OC) and total N (TN) in soil and fractions of SOM over time, soil samples were collected in the 0–5 and 5–10 cm layers, with the initial sampling done prior to the application of sunn hemp residues and ammonium sulfate. Five samples were collected every 2 months after the application of the legume and ammonium sulfate. The soil samples were submitted to densimetric and granulometric fractionation, obtaining the free light organic matter (F-LOM), particulate organic matter (POM), and organic matter associated with minerals (MAM). OC and TN stocks were then determined in soil and the SOM fractions. The changes in the stocks of OC (?StcC) in the soil in relation to time zero were positive in the evaluations carried out in the two layers. The fractions of SOM showed positive ?StcC at almost all of the evaluated times. The N supplied to the soil in the form of mineral and organic fertilizer promoted an increase of 0.24 Mg ha-1 of N in the 0–5 cm layer until after 60 days. Of this total, 0.03 Mg ha-1 was associated with F-LOM, 0.07 Mg ha-1 with POM, and the remainder was associated with MAM. Nearly 60% of the N that was supplied to the soil was drawn to the stable fractions of the SOM, indicating a rapid stabilization of this nutrient in the most recalcitrant organic compartments. Despite that, the variations in N stocks of MAM became smaller over time, and eventually became negative, in relation to time zero. This indicates the mineralization of N of this compartment. In the 5–10 cm layer, no effect of time was observed in the soil TN, N-POM, or N-MAM stocks. Additionally, under the conditions of this experiment, the majority of the N supplied to the soil was rapidly incorporated into the most stable fraction of SOM, and this might can reduced the efficiency of the green manuring.