<p>Biodiversity is fundamental for sustainability, providing ecosystem services that support agricultural productivity and long-term ecosystem resilience. However, the factors that link the internal structure of cocoa agroecosystems with the surrounding landscape and their influence on plant biodiversity and production performance remain poorly under-stood in tropical regions, limiting the design of effective strategies to balance conservation and productivity. This study examines 32 cocoa agroecosystems in Boyacá, Colombia, integrating field assessments of cocoa agroforestry systems (CAFS), Main Agroecological Structure (MAS), adjacent landscape fragmentation, and crop performance evaluation. Relationships among variables were examined using Mantel tests and Principal Component Analysis to reveal multiscale patterns connecting farm management, biodiversity, and landscape configuration. The analysis revealed four main findings: (1) 59% of the agroecosystems exhibited moderately developed MAS with heterogeneous landscape cohesion and connectivity; (2) distinct groups of farms were identified based on internal crop characteristics and their areas of influence, but no association was found between farm-level attributes and overall landscape structure; (3) a negative relationship emerged between landscape conservation and crop biodiversity, with farms hosting greater species richness located in less fragmented landscapes; and (4) despite moderate connectivity favorable for biodiversity, cocoa production remained below expected national averages. These findings highlight that integrating farm-level characteristics with landscape metrics is essential to enhance sustainability in cocoa production systems. Promoting shade management, fostering stakeholder collaboration, and implementing compensation mechanisms can strengthen biodiversity conservation while supporting production, providing actionable guidance for agroforestry-based strategies in tropical cocoa landscapes.</p>