Coral reefs worldwide have shown significant decline in biodiversity and structural complexity in the last 50 years. Hence, it has become an impetus in marine science to identify coral reef areas to protect and conserve for ecological and economic purposes. In the Philippines, threats to corals and its associated communities are more pronounced near population centers and relatively less on offshore oceanic reefs. However, these less accessible offshore reefs remain vulnerable to direct resource extraction, Acanthaster predation, bleaching, and typhoons. In Apo Reef Natural Park (ARNP), these perturbations have occurred at short intervals and resulted to significant changes in the reefscape. In the last 13 years, ARNP has experienced two cycles of Acanthaster outbreaks that were closely followed by strong typhoons. These consecutive disturbance have resulted in notable changes in the reef complex’s benthic features, with hard corals showing uneven but consistent decline across established monitoring stations. Thus, it has become a government priority to improve our understanding of the ecological processes that underlie recovery and resilience of ARNP. Historical data has shown that protection from extractive activities is not sufficient to ensure hard coral recovery and the maintenance of topographic complexity in ARNP. It has become imperative to craft and implement science-based management strategies that are cost effective in achieving specific conservation targets. In the study, important ecological processes have been elucidated through regular community monitoring activities and the conduct of assisted rehabilitation experiments. The results of the study showed three important findings. First, the recovery of hard corals after a major disturbance is slow in ARNP. Second, protection from intense fishing pressure is essential in maintaining the community structure of the reef’s associated fish and invertebrate assemblages. The relative health of these communities is seen to contribute to coral community recovery in the reef complex. Lastly, assisted substrate stabilization in a high energy reef environment is slow and possible only in certain areas of ARNP. The study supports the continued strict protection of the reef complex from extractive activities. In addition, active substrate rehabilitation activities must be improved and implemented together with other techniques that enhance coral growth and substrate complexity. It is clear that aside from enforcing the no-take policy in the reef complex, investing on adaptive management strategies is essential in ARNP.