<p>Philippine coral reefs have significantly declined over the past 40&#xa0;years, resulting in reduced coral cover and shifts in the composition of associated organisms. While research on offshore reef systems often focuses on benthic habitat cover and reef fish, limited information remains on post-disturbance macroinvertebrate communities at a local scale. This study examines the impacts of two tropical cyclones on benthic macroinvertebrate communities in Apo Reef Natural Park (ARNP), Philippines. Typhoons Molave and Goni passed through ARNP between October and November 2020, causing extensive reef damage, particularly to structurally complex branching corals. Despite observed benthic changes, macroinvertebrate abundances increased over time, primarily driven by generalist taxa such as camarodont urchins, decapod crustaceans, and ophiuroids. In contrast, coral-dependent groups, including filter feeders and corallivores, were more sensitive to coral loss. Multivariate analyses confirmed that macroinvertebrate community composition had shifted 3&#xa0;years after the consecutive disturbances. These findings, supported by univariate models, also revealed strong associations with benthic cover such as hard coral, algae, and coralline pavement. The study highlights how bottom-up controls, through reef-scale changes, influence shifts in benthic macroinvertebrate community structure, with additional variation potentially driven by invertivore reef fishes. Continued monitoring of macroinvertebrate communities is recommended to yield meaningful information at a temporal scale that complements hard coral recovery.</p>