A novel method for the determination of linear and cyclic siloxane compounds (L2, L3, D3, D4, D5, and D6) in biogas was developed by combining gas chromatography (GC) with inductively coupled plasma mass spectrometry (ICP-MS). Using a continuous liquid quench sampling system, biogas samples were collected from a Swiss biogas production plant processing manure and mixed organic wastes. Although significant concentrations of siloxanes are normally linked to biogas from wastewater treatment plants (WWTP) or landfill gas, manure and mixed organic waste samples also showed values in the range of 0.1 mgSi Nm−3, which would be particularly critical for appliances such as solid oxide fuel cells (SOFC). The GC-ICP-MS method showed very good linearity for all the investigated compounds (R2 between 0.999 and 1.000). The limits of detection and quantification (LOD and LOQ) in the gas for cyclic compounds, such as D5, vary based upon the used sampling conditions (approximate range of 0.002–0.004 mgSi Nm−3 and 0.007–0.014 mgSi Nm−3, respectively). To the best of our knowledge, these LOD and LOQ values are by far among the lowest reported in literature and they satisfy the EURAMET (the European Association of National Metrology Institutes) requirements, which fix recommended levels for Si total amounts between 0.1 and 0.3 mgSi Nm−3 for measurement in biogas or bio-methane. The GC-ICP-MS method was evaluated by comparing its performances with a flame ionization detector (FID), operated in parallel with ICP-MS, and with GC-MS (gas chromatography - mass spectrometry). The GC-FID showed higher detection limits and matrix effects than GC-ICP-MS. Nevertheless, it can still be suitable for an initial estimation of the siloxane compounds present in the biogas, at least for samples having relatively high concentration, by following some data treatment optimization. The GC-MS analyses were considered here as a further confirmation of the accuracy of the GC-ICP-MS results.