Enteric methane production from livestock is an important source of anthropogenic greenhouse gas emissions. The aim of the present study was to (1) assess the effect of long-term breeding for kilograms of milk fat plus protein production and (2) investigate the influence of parity, genetic line and diet on predicted enteric methane emissions of Holstein Friesian dairy cows. Analyses were based on 17 years of experimental data for lactating and dry cows, housed and at pasture. Restricted maximum likelihood (REML) was used to assess the effects of parity, genetic line and diet on the predicted enteric methane output of lactating and dry cows. A non-linear equation based on metabolisable energy intake (MEI) was used to predict daily enteric methane output. The present study found that selection for kilograms of milk fat plus protein production, zero-grazing low-forage diets and maintaining persistently high-yielding older cows can reduce a cow’s enteric methane emissions per kilogram milk by up to 12%, on average. Comparing the first 5 years to the most recent 5 years of the study period showed that large savings of 19% and 23% in enteric methane per kilogram milk were made in cows selected for milk fat plus protein or selected to remain close to the average genetic merit for milk fat plus protein production for all animals evaluated in the UK, respectively. Additionally, management to minimise the length of the drying-off period can help reduce enteric methane emissions during a cow’s lactation period.