Cocoa production in Alto Beni, Bolivia, is a major source of income and is severely affected by climate change impacts and other stress factors. Resilient farming systems are, thus, important for local families. This study compares indicators for social–ecological resilience in 30 organic and 22 nonorganic cocoa farms of Alto Beni. Organic farms had a higher tree and crop diversity, higher yields and incomes, more social connectedness, and participated in more courses on cocoa cultivation. Resilience was enhanced by local farmers’ organizations, providing organic certification and supporting diversified agroforestry with seedlings and extension, going beyond basic organic certification requirements.