The long-term (>12 months) effect of fat supplementation on methane (CH4) output and rumen microbiota was measured in dairy cows. Twenty lactating dairy cows were fed indoor with grass silage/hay (Period 1), then outdoor with pasture-based diets (Period 2), and allocated to three dietary treatments for two consecutive entire lactations. Diets were not supplemented (C) or supplemented with 2-3% dry matter of extruded linseed (EL) or extruded rapeseed (ER). Individual intake, milk and CH4 production (sulphur hexafluoride tracer technique) were measured on five consecutive days in both periods. Rumen pH, volatile fatty acid (VFA) concentrations and microbial numbers were measured on rumen fluid samples collected before feeding. For both periods, CH4 yield (g/kg dry matter intake) was lower for EL (-15%; P <0.001), and numerically higher for ER (+14%) compared to C. The unexpected effect of ER on CH4 emissions remains difficult to explain. Measured as g/kg fat corrected milk, CH4 output remained lower for EL (-26%, P <0.05) than for C and ER, for both periods. Diet EL did not modify rumen VFA profiles and microbial numbers compared to C. Our work highlights the long term efficacy of EL supplementation of grass-based diets as a CH4 mitigation option.