Agroecology systems integrate social and ecological principles into agricultural practices. Current assessments do not adequately consider animal welfare. This study introduces a new agroecology assessment tool by adding livestock sustainability and animal welfare criteria based on the Five Domains. Through a cross-sectional survey of 14 case studies, we examine how livestock sustainability and animal welfare are integrated into agroecological systems. Surveyors gathered data from farms in Kenya (10), Thailand (1), Italy (1), Vietnam (1), and Mexico (1). Results indicate that certain management practices within agroecological systems, specifically import of feed edible for human consumption, impact sustainability and painful beak trimming and stressful transport, negatively impact animal welfare. These findings highlight the need to strengthen agroecological assessment methods by including sustainability and animal welfare indicators. Doing so can help drive food-system change that improves health, reduces disease risk, and enhances animals’ ecological and social contributions. The paper concludes that better policy and knowledge are essential to improving the wellbeing of both animals and farmers in agroecological systems. The integrated tool could help researchers and farmer organizations improve animal welfare on agroecological farms across different contexts. Better animal welfare could also support the wider adoption and scaling of livestock integration in agroecology.