Complex landscapes (i.e., those harboring multiple habitat types at immediate spatial proximity) are highly relevant to both applied and theoretical ecological research, yet the mechanisms shaping functional trait distributions and diversity metrics across trophic levels in these systems remain poorly understood. To address this knowledge gap, we used wood-pastures as a model system and focused on two prominent groups occupying different trophic levels: plants and ants. We sampled three Central-European wood-pastures, with all four encompassed habitat types (grasslands, solitary trees, forest edges, and forests; 48 sites in total). Our results revealed significant differences in taxonomic and functional composition for both groups among the different habitat types of wood-pastures. However, the underlying mechanisms driving these patterns differed between plants and ants. Based on RLQ and fourth-corner analyses, heterogeneity in environmental conditions mainly influenced plant functional trait distributions. In contrast, ant diversity metrics and trait distributions were strongly linked to vegetation characteristics and habitat structure, and were only indirectly influenced by local microclimate, as shown by path analyses. These highlight that while mapping the increased environmental heterogeneity of complex landscapes, the main mechanisms shaping functional composition and diversity metrics might differ for organisms at different trophic levels (i.e., predominantly environmental filtering for plants and interspecific competition for ants). Consequently, the patterns and peaks of taxonomic and functional diversity do not necessarily coincide for different organisms in complex landscapes, emphasizing that conservation initiatives should focus on the system as a whole, rather than individual habitat types, to maximize biodiversity conservation.