Homegardens are coupled social-ecological systems that act as biodiversity reservoirs while contributing to local food sovereignty. These systems are characterized by their structural complexity, while involving management practices according to gardener's cultural origin. Social-ecological processes in homegardens may act as filters of species' functional traits, and thus influence the species richness-functional diversity relationship of critical agroecosystem components like beetles (Coleoptera). We tested the species richness-functional diversity relationship of beetle communities and examined whether habitat structure across different levels, sociodemographic profiles, and management practices act as filters in homegardens in a Global Biodiversity Hotspot, Chile. For 100 homegardens (50 campesino and 50 migrant), we sampled beetles and habitat attributes, and surveyed gardeners' sociodemographic profiles and management practices. We recorded 85 beetle species and found a positive relationship between species richness and functional richness that saturated when functionally similar species co-occur more often than expected by chance, indicating functional redundancy in species-rich homegardens. Gardener origin (campesino/migrant), homegarden area (m2), structural complexity (index), and pest control strategy (natural, chemical, or none) were the most influential social-ecological filters that selectively remove beetle species according to their functional traits. We discuss opportunities in homegarden management for strengthening local functional diversity and resilience under social-environmental changes.