Antibiotic residues and antibiotic resistance genes can enter the environment via fertilization with calf and pig manure. In a longitudinal study, nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) and 56 antibiotic residues were investigated in 288 soil samples and 8 corresponding slurry samples from 6 pig farms and 2 veal farms using qPCR and LC-MS/MS, respectively. A significant increase in gene copy number of tet(M), erm(B), erm(F) and sul2 was observed in all the soil layers between sampling times prior to (T1) and 2-3 weeks after fertilization (T3). Tet(B), tet(Q) and tet(L) were least abundant in the soil among the genes tested. From 7 classes of antibiotics, 20 residues were detected in soil and slurry using an optimized and validated extraction method. Flumequine was detected in all soil samples in concentrations below 100 μg/kg despite being detected in only half of the corresponding slurry samples. Doxycycline, oxytetracycline, lincomycin and sulfadiazine were also frequently detected in concentrations ranging from 0.1 μg/kg to 500 μg/kg and from 2 μg/kg and 9480 μg/kg in soil and slurry, respectively. Furthermore a positive association between the presence of antibiotic residues (total antibiotic load) and antibiotic resistance genes in soil was found. One possible explanation for this is a simultaneous introduction of antibiotic residues and resistance genes upon application of animal slurry.