This study investigated the fate of antibiotics during composting and its relationship with organic matter fractionation. Sludge was spiked with roxithromycin (ROX), chlortetracycline (CTC), oxytetracycline (OTC), and ciprofloxacin (CIP), at 3 different levels. Accelerated solvent extraction (ASE) and liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) were used for the extraction and the quantification of antibiotics. Sludge composting effectively removed parent compounds (p < 0.01) such as ROX, CTC, and OTC (52–87, 69–95 %, and 100 % respectively), while CIP persisted in the final compost (p > 0.05). The thermophilic stage was responsible for ROX removal, and the maturation stage was more implicated in removing CTC and OTC. Chemical accessibility and 3D fluorescence showed that high level of antibiotics affected the behavior of organic fractions. ROX removal was more associated with decreasing the most accessible fractions. The removals of CTC and OTC was more associated with the depletion of the complex organic matter. The observed results were confirmed by PCA and dendrograms analysis that confirmed the relationship between antibiotics removal and the evolution of organic pools. On the other hand, germination test indicated that cress and turnip were more sensitive to high antibiotic concentration. These results have been explored for the first time and they are recommended for controlling antibiotic removal based on organic matter fractionation.