This study investigated the effects of supplementing 40 g lauric acid (C12) kg(-1) dry matter (DM) in feed on methane emissions from early-lactating dairy cows and the associated effects on methane, nitrous oxide and ammonia release from the manure during storage. Stearic acid (C18), a fatty acid without assumed methane-suppressing potential in the digestive tract of ruminants, was added at 40 g kg(-1) DM to a control diet. The complete feed consisted of forage and concentrate in a ratio of 1.5:1 (DM basis). The manure was stored for 14 weeks either as complete slurry or, separately, as urine-rich slurry and farmyard manure representing two common storage systems. Methane release of the cows, as measured in respiratory chambers, was lower with C12 by about 20%, but this was mostly resulting from a reduced feed intake and, partly, from a lower rate of fibre digestion. As milk yield declined less than feed intake, methane emission per kg of milk was significantly lower with C12 (11.4 g) than with C18 (14.0 g). Faeces of C12-fed cows had a higher proportion of undigested fibre and accordingly methane release from their manure was higher compared with the manure obtained from the C18-fed cows. Overall, manure-derived methane accounted for 8.2% and 15.4% of total methane after 7 and 14 weeks of storage, respectively. The evolution of methane widely differed between manure types and dietary treatments, with a retarded onset of release in complete slurry particularly in the C12 treatment. Emissions of nitrous oxide were lower in the manures from the C12 treatment. This partially compensated for the higher methane release from the C12 manure with respect to the greenhouse gas potential. The total greenhouse gas potential (cow and manure together) accounted for 8.7 and 10.5 kg equivalents of CO2 cow(-1) d(-1) with C12 and C18, respectively. At unaffected urine-N proportion ammonia and total nitrogen losses from stored manure were lower with C12 than with C18 corresponding to the differences in feed and nitrogen intake. The present results suggest that manure storage significantly contributes to total methane emission from dairy husbandry, and that the identification of effective dietary mitigation strategies has to consider both the digestive tract of the animals and the corresponding manure.