Biotic interactions and community structure are seldom examined in mass extinction studies but must be considered if we are to truly understand extinction and recovery dynamics at the ecosystem scale. Here, we model shallow marine food web structure across the Toarcian extinction event in the Cleveland Basin, UK using a trait-based inferential modelling framework. First, we subjected our pre-extinction community to extinction cascade simulations in order to identify the nature of extinction selectivity and dynamics. Second, we tracked the pattern and duration of the recovery of ecosystem structure and function following the extinction event. In agreement with postulated scenarios, we found that primary extinctions targeted towards infaunal and epifaunal benthic guilds reproduced the empirical post-extinction community. These results are consistent with geochemical and lithological evidence of an anoxia/dysoxia kill mechanism for this extinction event. Structural and functional metrics show that the extinction event caused a switch from a diverse, stable community with high levels of functional redundancy to a less diverse, more densely connected, and less stable community of generalists. Ecological recovery appears to have lagged behind the recovery of biodiversity, with most metrics only beginning to return to pre-extinction levels ~7 million years after the extinction event. This protracted pattern supports the theory of delayed benthic ecosystem recovery following mass extinctions even in the face of seemingly recovering taxonomic diversity.