In 2013, the remote Tubbataha Reef UNESCO World Heritage Site, in the western Philippines, experienced two ship groundings within four months: the USS Guardian (USSG), a US military vessel, and the Min Ping Yu (MPY), an illegal Chinese fishing vessel. Here, we present the results of coral disease assessments completed two years post-grounding and recovery patterns monitored annually within these grounding sites. Site assessments were undertaken in three distinct zones: 'ground zero', where reef was scoured to its limestone base by direct ship impact; the 'impact border', containing surviving upright but damaged, abraded and fragmented colonies injured during ship movement; and undamaged 'control' sites, remote from the ship groundings but located on the same atoll. Coral diseases were dominated by white syndromes, and prevalence was an order of magnitude higher within the impact border zones than within the other zones two years after the events. Hard coral cover has steadily increased at a mean rate of 3% per year within the scoured USSG site at a rate comparable to control sites. In contrast, recovery has been negligible within the rubble-dominated MPY site, suggesting that substrate quality strongly influenced recovery processes such as recruitment, as larvae do not survive well on unstable substrates. Long-term recovery trajectories from these two grounding events appeared strongly influenced by movement of the ship during and after each event, and site-specific wave-influenced persistence of rubble and debris. High prevalence of coral disease among damaged but surviving colonies two years post-grounding suggested long-term impacts which may be slowing recovery and creating localized pockets of higher persistent disease prevalence than that of the surrounding population.