Despite cocoa traditionally being grown in agroforestry systems, monoculture farming now dominates in major producing countries like Côte d’Ivoire and Ghana. Globally, interest is growing to return once more to cocoa agroforestry, due to its many benefits, including biodiversity conservation, temperature and water cycle regulation, and carbon sequestration. The article reports on a study which analysed cocoa agroforestry plots of smallholder farmers in Alto Beni, Bolivia. These systems are characterised by the high diversity and density of companion trees. The model plot, managed under dynamic agroforestry principles, showed variability in cocoa yields but these increased over time. Additional income was also yielded from companion crops, which provide timber for harvest and fruits for sale and consumption, improving income diversification, food security and food sovereignty. Dynamic agroforestry systems, therefore, have higher labour intensity but also higher income compared to monocrop cocoa production systems, which is supported by the the SysCom Bolivia trial of 2017–2019. Dynamic agroforestry systems are also shown to increase biodiversity, offer resilience against climate change, and improve farmer’s ratings of happiness. The article emphasises the importance of agroforestry systems for sustainable cocoa production, highlighting its provision of economic benefits alongside environmental and social advantages. To maximise the potential of agroforestry systems, there is a need for continued research and long-term data collection for continuous improvement of management practices.