Cross-breeding with European beef breeds has become a standard approach for the intensification of smallholder cattle production in Indonesia. This study assessed the environmental impact of cross-breeding, in terms of Global Warming Potential (GWP) and land use. We sampled 90 local Ongole and 162 cross-bred (Simmental × Ongole) cattle farms in four study areas. Expressed per kilogram of live weight of young stock produced, GWP (26.9 kg CO2–equivalents) and land use (34.2 m2) of farms with Ongole breeding stock were not significantly different from the GWP (28.9 kg CO2–equivalents) and land use (37.4 m2) of cross-bred farms. Cross-bred young stock grew faster, but in general cross-bred cattle required more feed. In the current smallholder production system, the dominant cross-breeding practice of using Simmental semen on Ongole and F1 cross-bred cows does not result in lower greenhouse gas emissions or land use per kilogram of live weight produced compared with farms with Ongole cows. The advantage from the faster growth of cross-breds is counteracted by the higher emissions from feed production for cross-breds.