Mutualistic interactions are essential for ecosystem functioning, such as seed dispersal of plants by animals (frugivory). However, it remains unclear how species extinctions impact interaction network architecture and interaction outcomes. Here, we developed a hierarchical rewiring model based on abundances, traits and phylogeny to identify which frugivory-related traits influence changes in networks and frugivore diets in response to plant species loss. We demonstrate that network architecture and diet are strongly influenced by the total reward and the consumption frequency of fruits with unique combinations of macronutrients. However, there was an uncoupling between network architecture and diet change, suggesting that different plant species modulate network structures and frugivore diets, and the ability of frugivores to shift partners reduced the impact of fruit loss on dietary outcome. Altogether, we reveal mechanistic links between extinctions, architecture and outcomes in mutualistic ecological networks, important to predict species interactions and ecosystem functioning in a changing world.