Antibiotics are widely used in animals for disease treatment and prevention. After use, these antibiotics end up in manure. Here we investigated the fate of veterinary antibiotics in animal manure during composting and their residues in manure-applied soils. The results showed that 64.7% of the detected veterinary antibiotics were removed after composting for 171 days, which mainly occurred at the thermophilic phase in the second week, followed by a long stable stage with limited variations. The removal rates for lincomycin, trimethoprim and the macrolides during the composting were >89.7%, while those for the sulfonamides, tetracyclines and fluoroquinolones were less than <63.7%. The dissipation of antibiotics during the composting was related to the change of compost physicochemical properties, especially moisture and C/N ratio. The application of compost products with antibiotic residues could still lead to soil contamination, which may pose risks of resistance selection to the soil ecosystem. Display omitted •17 veterinary antibiotics were detected during the 171 days of composting.•Tetracyclines and lincomycin were predominant in initial compost.•64.7% of detected antibiotics were removed during composting.•The removal of antibiotics mainly occurred in thermophilic phage.•Usage of compost product posed high risk of resistance selection in soil ecosystem.