Siloxanes are silicon-containing volatile organic compounds that occur in air, biogas and biomethane. Their presence in biogas and biomethane may give rise to silica deposits in gas transmission and distribution infrastructure, as well as in end-user appliances. The silicon concentration in biomethane is therefore regulated, and implementing these regulations requires reliable measurement methods and appropriate certified reference materials (CRMs) to calibrate analytical instruments. In this work, the primary measurement standards of two national metrology institutes are compared to assess their equivalence by means of gas chromatography analysis. The comparison addressed hexamethyldisiloxane (L2), octamethyltrisiloxane (L3), hexamethylcyclotrisiloxane (D3), octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5) in methane gas mixtures. Two mixtures were exchanged, one with siloxane amount fractions at the ppb-level as specified in the European specification EN 16723, and a second on ppm-level. The latter CRMs can be dynamically diluted or directly used to process concentrated biomethane samples. The results at both levels demonstrate equivalence in the preparation and analysis of the addressed siloxanes in methane.