With the current deforestation rates in tropical ecosystems, optimizing biodiversity in managed systems has become fundamental for conservation. Agroforestry has been suggested to conserve biodiversity and buffer deforestation rates, while also sustaining local livelihoods. While many studies have focused on the relation between local management intensity and biodiversity, processes at the landscape scale are often overlooked and remain a knowledge gap. In this study we identified drivers behind woody plant regeneration in coffee agroforestry on both local and landscape scale. We used univariate-, multivariate- and structural equation models to relate seedling species richness, diversity, density, community composition and height to local management intensity and location in the landscape of 60 coffee agroforestry sites in southwestern Ethiopia. Local management intensity, which simplifies and reduces canopy cover, negatively impacted species richness, diversity and density, presumably due to altered microclimatic conditions and a reduction in local seed sources. Seedling height was also reduced by management intensity, including slashing frequency and canopy cover. On the landscape scale, species richness and diversity of seedlings was higher at sites adjacent to continuous forests where seed sources are abundant, and declined with distance to the forest. In particular, late successional species were negatively affected, whereas common shade tree species and pioneers occurred as seedlings throughout the landscape and in more managed systems. This suggests that dispersal limitation is detrimental for the regeneration of late successional species, especially in agroforestry systems where the standing woody plant diversity is largely reduced. Our results indicate that natural regeneration of woody plants still occurs in coffee agroforestry systems, primarily when the canopy structure is dense and diverse and/or when sites are located nearby continuous forests. Management intensification and deforestation will limit the potential for many woody plant species to regenerate in coffee agroforestry sites, by altering the local microclimate, reducing local seed sources and disrupting seed dispersal from the surrounding landscape. This will likely result in a positive feedback loop, as a reduction in woody plant regeneration reduces future seed sources. We therefore stress that both a local and a landscape perspective should be incorporated in conservation and restoration approaches.