One of the key questions for agroecology is the practical evidence on enhancing biodiversity in specific contexts, primarily through agroecological enterprise combinations that challenge monocultures. This study provides an answer to this question through a case from Uganda, investigating the role of biodiversity in the transition of agroecosystems toward agroecology, with a focus on Bugala Island in Kalangala District. Using a qualitative interpretive approach, the methods involve document reviews, stakeholder engagement, focus group discussions, and expanding on the data previously reported about relevant policies such as the National Environment Management Policy (1995), Uganda Vision 2040, the National Agriculture Policy (2013), and the Uganda Biodiversity Strategy and Action Plan II. Results highlight key threats to biodiversity, including habitat loss and land-use changes driven by oil palm monocropping. From the previous work on Navigating the Policy Landscape in Uganda, results reveal gaps in integrating agroecological principles, such as biodiversity conservation and sustainable resource governance, into national agricultural strategies. This current study shows that stakeholder uptake of agroecological practices like intercropping and crop rotation is limited, with only 9% of farmers trained on biodiversity-friendly techniques, compared to 71% trained on monocropping methods. Despite these challenges, some farmers have embraced agroecological practices to enhance soil health, crop diversity, and ecosystem stability. Conclusions emphasize the critical role of biodiversity in achieving sustainable agricultural systems and the Sustainable Development Goals. Policy recommendations include improving farmer co-learning and agroecological practices and embedding biodiversity conservation into Uganda’s agricultural framework to foster food security, climate resilience, and equitable development.