Ruminants are central to the economic and nutritional life of much of sub-Saharan Africa, but cattle are now blamed for having a disproportionately large negative environmental impact through emissions of greenhouse gas (GHG). However, the mechanism underlying excessive emissions occurring only on some farms is imperfectly understood. Reliable estimates of emissions themselves are frequently lacking due to a paucity of reliable data. Employing individual animal records obtained at regular farm visits, this study quantified farm-level emission intensities (EIs) of greenhouse gases of smallholder farms in three counties in Western Kenya. CP was chosen as the functional unit to capture the outputs of both milk and meat. The results showed that milk is responsible for 80–85% of total CP output. Farm EI ranged widely from 20 to >1 000 kg CO$_{2}$-eq/kg CP. Median EIs were 60 (Nandi), 71 (Bomet), and 90 (Nyando) kg CO$_{2}$-eq/kg. Although median EIs referenced to milk alone (2.3 kg CO$_{2}$-eq/kg milk) were almost twice that reported for Europe, up to 50% of farms had EIs comparable to the mean Pan-European EIs. Enteric methane (CH$_{4}$) contributed >95% of emissions and manure ∼4%, with negligible emissions attributed to inputs to the production system. Collecting data from individual animals on smallholder farms enabled the demonstration of extremely heterogeneous EI status among similar geographical spaces and provides clear indicators on how low EI status may be achieved in these environments. Contrary to common belief, our data show that industrial-style intensification is not required to achieve low EI. Enteric CH$_{4}$ production overwhelmingly drives farm emissions in these systems and as this is strongly collinear with nutrition and intake, an effort will be required to achieve an “efficient frontier” between feed intake, productivity, and GHG emissions.