Soils are the largest terrestrial C pool on Earth. However, most studies only investigated soil organic carbon (SOC) storage on surface soils layers. This has resulted in lack of knowledge on SOC dynamics in deep soil layers despite the fact that they contain a significant portion of the stored organic C. This study assessed how contrasting land uses and agronomic practices affect SOC stocks up to a 5-m depth, and investigated superficial SOC concentration, and particle and density fractionation in a case study in the U.S. Southeastern Plains. On average, deep (90–500 cm) SOC accounted for 80% of total organic C across the investigated land-use systems. A close relation between SOC concentration and Mehlich-3 extractable Al and Fe concentration in deep soil samples suggested that non-crystalline metals play a key role stabilizing deep SOC in this system. Land use had a significant effect only on superficial SOC concentration, and light, heavy, and mineral associated organic C within micro and macroaggregates. Soils from native vegetation, and non-irrigated sod-based rotation plots showed greater concentrations of SOC in almost all assessed micro and macroaggregates fractions, whereas those from the conventional crop rotation and irrigated sod-based rotation plots showed lower SOC concentration in all assessed fractions.