Climate-smart approaches have gained momentum in tropical, agricultural development. However, to date, few studies have examined whole-farm greenhouse gas (GHG) balances in smallholder crop-livestock systems. This study aimed to quantify GHG balances at farm-scale, identify GHG hotspots and assess mitigation options in coffee-dairy farms undergoing agricultural intensification in Central Kenya. In recent decades, decreasing farm size has forced the shift from extensive practices to zero-grazing systems and higher nitrogen (N) inputs. We hypothesised that different farm strategies and intensification levels determine the farm's GHG balance. A farm typology was constructed through principal component analysis (PCA) and hierarchical clustering from 125 farms surveyed. Four farm types were identified ranging relatively from small to large farms, low to high livestock intensities, and low to high N input rates. Whole-farm GHG balances were estimated using an adapted version of the Cool Farm Tool (CFT). Farms were found to be net sources of GHG, averaging from 4.5 t CO2 eq ha-1 yr-1 in less intensive farms to 12.5 t CO2 eq ha-1 yr-1 in high intensive farms. Within the farm GHG hotspots identified, methane (CH4) from enteric fermentation processes accounted for 26–39% of total farm GHG emissions; nitrous oxide (N2O) and CH4 from manure management systems (MMS) for 26–38%; soil background and fertilizer induced N2O emissions for 24–29%; off-farm production of feeds and agrochemicals for 10–22%; and crop residue management (CRM) for the remaining 1–3%. Within the mitigation practices assessed, zero-grazing stalls already lowered the livestock maintenance energy requirements, reducing enteric fermentation emissions. Stall-feeding, however, brings the necessity-opportunity to manage the manure and our results showed that MMS can be a determining factor in the GHG balance. Increasing the frequency of manure collection from stalls in favour of solid storage systems can reduce N2