Methane (CH₄) is an important greenhouse gas. The growth of atmospheric CH₄ stalled from 1999 to 2006, with current explanations focussed mainly on changing surface fluxes. We combine models with observations and meteorological data to assess the atmospheric contribution to CH₄ changes. We find that variations in mean atmospheric hydroxyl concentration can explain part of the stall in growth. Our study highlights the role of multi-annual variability in atmospheric chemistry in global CH₄ trends.