The response of shallow-marine ecosystems to the Paleocene-Eocene Thermal Maximum (PETM) is understudied, and analyses that do exist typically focus on larger benthic foraminifera and coral-algal reef mound evolution. Here we investigate the dynamics of benthic marine assemblages across the PETM in the Kozina and Čebulovica sections (Slovenia) on the Adriatic Carbonate Platform. Our results show significant ecological changes associated with the PETM with a protracted recovery into Shallow Benthic Zone (SBZ) 6. The compositional change corresponds to the reduced dominance of red algae, a turnover in the dominant larger benthic foraminifera and increased assemblage homogeneity. These changes are not associated with a lithofacies transition, as a shift from reefal mounds to a foraminiferal-dominated carbonate platform occurs prior to the Paleocene/Eocene boundary. The investigated sections also show a transition from coral-algal mounds to microbial mounds during SBZ 4, but the main difference between these reef types is the increased dominance of the microbes. Moreover, there is no unequivocal evidence that either reef type persisted into the Eocene in this region. Whilst the PETM is not an extinction event, except for deep-sea benthic foraminifera, the ecological changes recorded show that the ecosystem responses at the PETM are consistent with other hyperthermal events.