Characterisation of biogases is normally dedicated to the online monitoring of the major components methane and carbon dioxide and, to a lesser extent, to the determination of ammonia and hydrogen sulphide. For the case of Volatile Organic Compounds (VOCs), much less attention is usually paid, since such compounds are normally removed during gas conditioning and with exception of sulphur compounds and siloxanes represent a rather low risk to conventional downstream devices but could be a hindrance for fuel cells. However, there is very little information in the literature about the type of substances found in biogases generated from biowaste or co-fermentation plants and their concentration fluctuations. The main aim of this study was to provide information about the time dependencies of the VOCs in three biogas plants spread out through Germany from autumn until summer, which have different process control, in order to assess their potential as biofuels. Additionally, this study was an attempt to establish a correlation between the nature of the substrates used in the biogas plants and the composition of the VOCs present in the gas phase. Significant time-dependent variations in concentration were observed for most VOCs but only small changes in composition were observed. In general, terpenes and ketones appeared as the predominant VOCs in biogas. Although for substances such as esters, sulphur-organic compounds and siloxanes the average concentrations observed were rather low, they exhibited significant concentration peaks. The second biogas plant which operates with dry fermentation was found to contain the highest levels of VOCs. The amount of total volatile organic compounds (TVOCs) for the first, second and third biogas plants ranged from 35 to 259 mg Nm−3, 291–1731 mg Nm−3 and 84–528 mg Nm−3, respectively.