This paper investigates the relationship between vascular plant production and CH4 emissions from an arctic wet tundra ecosystem in north-east Greenland. Light intensity was manipulated by shading during three consecutive growing seasons (1998–2000). The shading treatment resulted in lower carbon cycling in the ecosystem as mean seasonal net ecosystem exchange (NEE) decreased from −336 to −196 mg CO2 m−2 h−1 and from −476 to −212 mg CO2 m−2 h−1 in 1999 and 2000, respectively, and total ecosystem respiration decreased from 125 to 94 mg CO2 m−2 h−1 in 1999 and from 409 to 306 mg CO2 m−2 h−1 in 2000. Seasonal mean CH4 emissions in controls and shaded plots were, respectively, 6.5 and 4.5 mg CH4 m−2 h−1 in 1999 and 8.3 and 6.2 mg CH4 m−2 h−1 in 2000. We found that CH4 emission was sensitive to NEE and carbon turnover, and it is reasonable to assume that the correlation was due to a combined effect of vegetative CH4 transport and substrate quality coupled to vascular plant production. Total above-ground biomass was correlated to mean seasonal CH4 emission, but separation into species showed that plant-mediated CH4 transport was highly species dependent. Potential CH4 production peaked at the same depth as maximum root density (5–15 cm) and treatment differences further suggest that substrate quality was negatively affected by decreased NEE in the shaded plots. The concentration of dissolved CH4 decreased in the control plots as the growing season progressed while it was relatively stable in the shaded plots. This suggests that a progressively better developed root system in the controls increased the capacity to transport CH4 from the soil to the atmosphere. In conclusion, vascular plant photosynthetic rate and subsequent allocation of recently fixed carbon to below-ground structures seemed to influence both vegetative CH4 transport and substrate quality.