Quantitative and qualitative changes in organic matter were studied at different stages of treatment in a bioreactor designed to process leachates from a municipal solid waste landfill. The particulate matter (PM) and macromolecular fractions of the dissolved organic matter with solubility properties comparable to humic (acid-insoluble) and fulvic (acid-soluble) acid fractions (AI, AS, respectively) from the incoming black liquid, the bioreactor content, and the final processed effluent were isolated, quantified, and characterized by visible and infrared (IR) spectroscopies. The macromolecular signature either aliphatic (glycopeptides, carbohydrates) or aromatic (coinciding with infrared patterns of lignin, tannins etc.) enabled us to characterize the different organic fractions during the course of microbial transformation. The results reveal significant changes in the nitrogen speciation patterns within the different organic fractions isolated from the wastewater. The final increase in the relative proportions of nitrogen in the least aromatic AS fraction during microbial transformation could be related to protein formation inside the bioreactor. After biological treatment and ultrafiltration, the amount of organic matter was reduced by approximately 70%, whereas aromaticity increased in all fractions, indicating preferential elimination of aliphatic wastewater compounds. Most of the remaining fractions at the end of the process consisted of a yellow residue rich in low molecular weight AS fractions.