The soils in the NE of the Magdalena province (Colombia) are subject to intense degradation primarily because of the low accumulation rate of soil organic matter (SOM) and its fast turnover. Numerous traditional studies have aimed to mitigate this situation, focusing on the analysis of total SOM contents. The present study aimed to determine SOM quality from six areas under humid and dry tropical forest with different pedoclimatic conditions, using molecular characterization. For each area, sites with different current land use were studied, including forest and cultivated sites. We applied analytical pyrolysis (pyrolysis-GC/MS) to aqueous NaOH-extractable SOM from surface soil samples. One-hundred and ten pyrolysis products were identified and quantified, from the following chemical groups: N-containing compounds (34.1 ± 5.1%), carbohydrate markers (21.1% ± 7.1%), monocyclic aromatic compounds (20.0% ± 4.5%), aliphatic compounds (7.7% ± 1.4%), phenols (7.0% ± 5.0%), polycyclic aromatic compounds (3.6% ± 0.9 %), lignin products (0.3% ± 0.3%) and other compounds (0.2% ± 0.1%). SOM of all studied areas showed a large proportion of N-containing products, indicating a high contribution from microbial material to the SOM. Multivariate statistics allowed for the differentiation between microbial-derived and plant-derived SOM (Factor 1) and the relative proportion of burning residues (Factor 2), and indicated that pedoclimatic conditions exert more influence on SOM composition (cool and humid zones were enriched in microbial SOM while dry zones contained more plant-derived SOM) than land use for the studied soils.