Abstract. With the densification of surface observing networks and the development of remote sensing of greenhouse gases from space, estimations of methane (CH4) sources and sinks by inverse modelling face new challenges. Indeed, the chemical transport model used to link the flux space with the mixing ratio space must be able to represent these different types of constraints for providing consistent flux estimations. Here we quantify the impact of sub-grid scale physical parameterization errors on the global methane budget inferred by inverse modelling using the same inversion set-up but different physical parameterizations within one chemical-transport model. Two different schemes for vertical diffusion, two others for deep convection, and one additional for thermals in the planetary boundary layer are tested. Different atmospheric methane datasets are used as constraints (surface observations or satellite retrievals). At the global scale, methane emissions differ, on average, from 4.1 Tg CH4 per year due to the use of different sub-grid scale parameterizations. Inversions using satellite total-column retrieved by GOSAT satellite are less impacted, at the global scale, by errors in physical parameterizations. Focusing on large-scale atmospheric transport, we show that inversions using the deep convection scheme of Emanuel (1991) derive smaller interhemispheric gradient in methane emissions. At regional scale, the use of different sub-grid scale parameterizations induces uncertainties ranging from 1.2 (2.7%) to 9.4% (14.2%) of methane emissions in Africa and Eurasia Boreal respectively when using only surface measurements from the background (extended) surface network. When using only satellite data, we show that the small biases found in inversions using GOSAT-CH4 data and a coarser version of the transport model were actually masking a poor representation of the stratosphere–troposphere gradient in the model. Improving the stratosphere–troposphere gradient reveals a larger bias in GOSAT-CH4 satellite data, which largely amplifies inconsistencies between surface and satellite inversions. A simple bias correction is proposed. The results of this work provide the level of confidence one can have for recent methane inversions relatively to physical parameterizations included in chemical-transport models.