A new method for the analysis of sulfonamides and tetracyclines in heterogenic biogas plant input samples and fermentation residues is introduced. Veterinary antibiotics are only partially absorbed in the animal gut; therefore, animal manure can contain high loads of these substances. Animal manure is used for biogas generation, so antibiotics can enter the anaerobic fermentation process this way. However, only little is known about the fate of antibiotics within this process, also due to the lack of suitable analytical methods for this complex sample matrix. Therefore, we developed a method for the analysis of ten sulfonamides (sulfachloropyridazine, sulfadiazine, sulfadimethoxine, sulfaguanidine, sulfamerazine, sulfamethazine, sulfamethoxazol, sulfamethoxypyridazin, sulfapyridine, sulfathiazole) and four tetracyclines (chlortetracycline, doxycycline, oxytetracycline, tetracycline) in biogas plant input and output samples, including a single liquid-liquid-extraction step and analysis via liquid chromatography (LC) and triple quadrupole mass spectrometry. The detection limit of this method ranges from 0.01 to 0.08 mg kg(-1). Matrix calibration using antibiotic-free cattle feces and isotopic-labeled internal standards enables quantification of antibiotics in different matrices such as animal manure, dung, or fermenter outputs with recovery rates between 70 and 130 %. This makes the method suitable for investigating the fate of antibiotics in animal manure and fermentation processes. A screening of 15 German biogas plants revealed the presence of several antibiotics up to 9 mg kg(-1) (201 mg kg(-1) dry matter). During the fermentation process, elimination occurs; however, with the exception of chlortetracycline, the antibiotic content remains in the same order of magnitude.