It is currently uncertain as to whether methane exists on Mars. Data from the Curiosity Rover suggests a background methane concentration of a few tenths parts per billion whereas data from the Trace Gas Orbiter suggest an upper limit of twenty parts per trillion. If methane exists on Mars then we do not understand fully the physical and chemical processes affecting its lifetime. Atmospheric models suggest an over-estimate in the lifetime by a factor of around six hundred compared with earlier observations. In the present work we assume the Curiosity Rover background methane value and estimate the uncertainty in atmospheric chemistry and mixing processes in our atmospheric column model 1D TERRA. Results suggest that these processes can only explain a factor of ~sixteen lowering in the methane lifetime. This implies that if methane is present then additional, currently unknown processes are required to explain the observed lifetime. •Uncertainties in photochemical rates and mixing lead to a factor ~ sixteen lowering in methane.•Methane is removed via photolysis at less than about 0.01 hPa and via hydroxyl and excited atomic oxygen at greater pressures.•Dissociation by low energy electrons does not strongly affect methane but could impact the biosignature nitrous oxide.•The effect of galactic cosmic rays upon atmospheric composition is small, up to a few percent.•Strong ground level events in HEPs lead to a change (at 1.4 km height) in NOy of up to a few ppbv and up to 10 ppmv in HOx.