Sandy soils in tropical climates with low organic matter (OM) content result in degradation and fertility loss. It is important to note that humified OM accumulation and stabilization increases soil fertility. This study aimed to characterize humic acids (HAs) in sandy soils on an agroecological farm operating for more than 20 years. The structures of the HA of two Planosols under a grazing (G) and crop rotation (R) management system and of an Acrisol under an agroforestry management system (AFS) were characterized using HA extracted from a local Organosol under cassava monoculture (M) as a structural reference. Lower CHA/CFA ratio in sandy soil reveals a slightly humified OM and higher E4/E6 ratio value in HA confirming lower aromatic structure condensation. The HA in Planosols (R and G) and Acrisols (AFS) are predominantly formed by CAlq‐O,N–, CAlq‐O–, and CAlq‐di‐O structures closely related to the soil physical properties and preserved by interaction with the mineral fraction confirmed by νO‐H, νSi‐O stretching of kaolinite and hematite bands in FTIR spectroscopy. Management and vegetal carbon type (−20.65‰ AFS ‐C3) or (−15.55‰ (G) and −17.82‰ (R) ‐C4) had no effect on HA formation. Evolution of structural change in HA modeled by chemometric analyses showed that more recalcitrant structure characteristic in HA can enhance OM preservation in these sandy soils. This study elucidated the OM stabilization mechanisms of sandy soil HA, their relationship with soil properties and models structural changes for humified OM recovery and preservation, which contribute to increased fertility and agricultural production.