Agricultural areas under integrated production systems, such as Integrated Crop-Livestock-Forest System (CLFS), have the potential to sequestrate carbon (C) since both Soil Organic Matter (SOM) content and trees biomass increase thus mitigating the emission of greenhouse gases (GHGs) from agriculture. Regarding soil aspects, the C content stands out as the main indicator, but the structural aspect of SOM is also relevant since it plays a key role in the chemical stability of C compounds and the soil lifetime of C compounds. Laser-Induced Fluorescence Spectroscopy (LIFS) is an effective technique to evaluate the SOM humification index (HLIFS) from practically intact whole soil samples under different agricultural systems. Thus, the objective of this study was to analyze the SOM humification index in different integrated systems, such as Integrated Crop-Livestock-Forest System (CLFS), Integrated Livestock-Forest System (LFS), Integrated Crop-Livestock System (CLS), and in references areas, such as Intensive Pasture (INT), Extensive Pasture (EXT) and Native Forest (NF). For this purpose, samples of Red-yellow Latosol (Haplorthox by Soil taxonomy) from the experimental site located at Embrapa Pecuária Sudeste (Southeast of Brazil) were collected five years after the establishment of the integrated systems. Samples were collected at soil depths of 0–5, 5–10, 10–20, 20–30, 30–40, 40–60, 60–80, and 80–100 cm. Pellets of the whole soil samples were prepared for LIFS analysis. In these areas, SOM humification indices (HLIFS) presented the following descending order: CLS > EXT > INT > LFS > CLFS > NF. Previous results have shown a greater soil organic carbon stock in these integrated production systems than in the NF area, suggesting C sequestration in agricultural soil. In the present study, SOM was classified by LIFS as more chemically stable in integrated production systems than in native vegetation. Higher amounts of fluorescent compounds were identified from LIFS data, probably resulting from condensed aromatic groups. SOM with more recalcitrant groups normally has a longer lifetime in the soil, indicating a long-term contribution to mitigating climate change by avoiding fast SOM decomposition and CO2 return to the atmosphere. Also, for the first time, this study was able to identify a positive correlation (R = 0.79) between the SOM humification index (HLIFS) and the Cation Exchange Capacity (CEC)/C content ratio of whole soil samples, another innovative contribution from soil LIFS analyses.