Understanding the relationship between the aerobic transformation of organic matter (OM) and the bioavailability of lead to plants may allow the safe application of organic fertilizers (OF) in agriculture. The present study aimed to elucidate the relationship of different OM structures with Pb, revealing the action of OF (poultry litter) on Pb dynamics, presenting the effects of OM transformations on bioavailability and transfer to vegetables produced in tropical mountain agroecosystems (TMA). The association of Pb with hydrophilic structures (CAlk-O and CAlk-di-O) during the aerobic transformation of poultry litter (PL) contributes to the increase in the water-soluble form of this metal (3.17-15.30%). The structural changes promoted by the transformation of OM, in addition to reducing the adsorption capacity of Pb in PL (Kd reduction from 1135.50 to 87.49), favor the formation of outer-sphere complexes. PL that have a more labile structure, i.e., those that are less humified, have greater affinity for Pb. The greater affinity of Pb for labile structures that are preserved in PL during OM transformations contributed to its increase and transport to edible plant parts. Considering the edible parts of vegetables grown in TMA and fertilized with fresh PL, 100% of broccoli, 91.78% of cabbage, 80.00% of tomato, 65.96% of parsley, 49.19% of lettuce, and 32.88% of cauliflower showed Pb contamination that exceeded the permitted level. Therefore, OF contributes to lead contamination of food produced in TMA, representing a risk to human health. Studies are needed to propose additional treatments for this residue before its use.