<p>Earthworms able to process and rework mineral soil layers (‘geoengineering’ earthworms) are currently expanding their range in arctic ecosystems. Recent assessments suggest that geoengineering earthworms alter the terrestrial carbon (C) balance of arctic ecosystems by affecting ecosystem productivity and respiration, effects that could be generated simultaneously or at different times of the growing season. In this study, we test if these earthworms affect the seasonal shift in CO₂ net ecosystem exchange (NEE), gross primary production (GPP), and ecosystem respiration (ER) in the tundra. Over 2 years, we measured the effect of <i>Aporrectodea</i> spp. and <i>Lumbricus</i> spp. on CO₂ exchange processes in two contrasting tundra vegetation types (heath and meadow) in a common garden experiment. We observed expected seasonal differences in GPP and ER with higher, GPP driven, uptake of CO₂ in the peak growing season compared to the end of the season. Earthworm presence did not change ecosystem C fluxes during early and peak season but led to a greater ecosystem uptake of CO₂ (NEE—45%) near the end of the growing season in both vegetation types. This late growing season increase in ecosystem CO₂ uptake correlated positively with greener vegetation with earthworm presence, but was diminished during a summer with severe drought. We, therefore, suggest that the CO₂ flux is driven by a change in plant phenology caused by earthworm activity extending late season photosynthesis, but that the strength of this effect is climate dependent. Our findings illustrate that geoengineering earthworms can impact plant phenology to generating a CO₂ flux that acts to counter the increased respiration losses expected to accompany warming autumns and an extended thawing period in the Arctic.</p>