A genetic impact assessment (GIA) methodology is developed, consisting of consultation of stakeholders, identification of issues and assessment of associated indicators, for crossbreeding with exotic beef breeds in smallholder mixed farms. The GIA is implemented in two case studies of crossbreeding with Limousin and Simmental in Madura and Central Java, Indonesia. Consultation of stakeholders (n = 421) in focus group discussions yielded the issues that should be taken into account in a GIA. Farmers identified economic benefits, feed availability, cattle management, animal’s performances, additional functions of cattle, and health and fertility as issues. Policymakers mentioned the production of beef as the main issue while scientists called for environmental quality and maintaining local farm animal genetic resources as issues. Indicators to characterize these issues in a GIA were deducted from literature; determination of the indicators was based on data sampled on 97 farms, keeping local Madura or Limousin crossbreds, in Madura and 252 farms and keeping local Ongole or Simmental crossbreds, in Central Java. The GIA showed that crossbreeding contributes to increased meat production at the national level; however, it does not necessarily guarantee improvements in economic benefits at farm level nor environmental performances.