Soil organic matter (SOM) is a dynamic soil property, sensitive and responsive to many factors. The possibility of increasing soil carbon (C) sequestration by changing land use and management practices has been of great interest recently due to concerns with global changes in the atmospheric carbon dioxide (CO2) balance. Nonetheless, as a result of the complex dynamics of SOM, there is still the need for SOM characterization procedures capable of monitoring SOM stabilization, taking into account all the factors involved. This study characterized SOM stabilization as affected by management practices in three long-term field experiments, considering physical, chemical and biological components. The field experiments are located near Lexington, Kentucky, on a Maury silt loam (fine, mixed, mesic Typic Paleudalfs). The first experiment evaluates tillage and nitrogen (N) rate effects. The second experiment studies manure and N rate effects. The third experiment evaluates the five corn components of three crop rotations [continuous (monoculture) corn, corn-wheat/double crop soybean, and hay-hay-corn-corn-corn]. Soil organic matter content, stability, and composition, for physically separated fractions, were assessed using δ13C natural abundance and diffuse reflectance Fourier transformed infrared (DRIFT) spectroscopy. In addition, management effects on microbial biomass and microbial function as indicated by phenol oxidase enzyme activity were evaluated. The results indicate that management practices affect SOM content, stability, and composition, and these effects differ by the soil aggregate fraction. No-tillage (NT), N fertilization, manure application and increased corn in crop rotations enhanced SOM levels. However, the effect of NT was observed mainly at the soil surface. Soil organic matter storage was determined by the aggregate size distribution. The proportion of recently deposited C was generally positively related to aggregate size, especially for the first and third experiments. Most of the recently deposited C was stabilized in microaggregates within macroaggregates, across the management treatments and field experiments. In addition, this fraction consistently exhibited low to medium SOM reactivity. These results suggest that SOM stabilization, as influenced by management practices, required achieving a specific composition and location within the soil matrix. This implies that soil C forms and aggregate size and stability are closely interrelated.