Mega-diverse coral reef ecosystems are declining globally, necessitating conservation prioritizations to protect biodiversity and ecosystem services of sites with high functional integrity to promote persistence. In practice however, the design of marine-protected area (MPA) systems often relies on broad classifications of habitat class and size, making the tacit assumption that all reefs are of comparable condition. We explored the impact of this assumption through a novel, pragmatic approach for incorporating variability in coral cover in a large-scale regional spatial prioritization plan.