The impact of contrasting land use types on the soil methane (CH4) sink remains elusive. We examined for the first time how annual versus perennial grain cropping influences CH4 fluxes. Experimental sites were located in Edmonton and Breton, Canada. Treatments included perennial-forage, perennial-grain, fall-grain, spring-grain and fallow. We measured CH4 fluxes at soil surface, as well as root density, temperature and moisture at multiple soil depths over two years. Overall, Breton was a 58% larger CH4 sink than Edmonton. Moreover, clear differences across cropping systems were evident in Edmonton. Both perennial-grain and perennial-forage were stronger CH4 sinks than both spring-grain and fallow (P < 0.01). Notably, perennial-grain was a 67% stronger CH4 sink than spring-grain (444 vs. 265 g CH4-C ha−1 over two growing seasons). These divergences were indiscernible in Breton, where all cropping systems sustained uniformly higher CH4 sinks. The sites responded differently to the same cropping systems likely due to their contrasting land use histories. A long-term cropping of perennial forages prior to experiment establishment in Breton was conducive to maintaining a higher CH4 sink, masking treatment effects. Conversely, a background of recurrent annual cropping (as in Edmonton) resulted in an enhanced CH4 sink when transitioning into perennial-grain. The Q10 responses of the daily CH4 fluxes to temperature further pointed to the greater CH4 sink by perennial-grain. Irrespective of site, perennial-grain had a Q10 at least 24% larger than spring-grain. Additionally, perennial-grain had deeper-denser roots and lower water-filled pore space (WFPS) by 19% than spring-grain, likely enhancing gas exchange through the perennial-grain soil profile. The highest sensitivity of CH4 fluxes to temperature and WFPS emerged from measurements taken at 40 cm depth, suggesting peak CH4 consumption at this subsurface layer. Overall, results indicate that as a consequence of increased root growth, perennial-grain can favorably shift the aeration-moisture balance in the soil towards increased CH4 uptake.