Marine heatwaves are causing recurring coral bleaching events on tropical reefs that are driving ecosystem change. Yet, little is known about how bleaching and subsequent coral mortality impacts the spatial properties of tropical seascapes, such as patterns of organism spatial clustering and heterogeneity across scales. Changes in these spatial properties can offer insight into ecosystem recovery potential following disturbance. Here we repeatedly quantified coral reef benthic spatial properties around the circumference of an uninhabited tropical island in the central Pacific over a 9‐year period that included a minor and subsequent severe marine heatwave. Benthic communities showed increased biotic homogenisation following both minor and mass bleaching, becoming more taxonomically similar with less diverse intra‐island community composition. Hard coral cover, which was highly spatially clustered around the island prior to bleaching, became less spatially clustered following minor bleaching and was indiscernible from a random distribution across all scales (100–2000 m) following mass bleaching. Interestingly, the reduced degree of hard coral cover spatial clustering was already evident by the onset of mass bleaching and before any dramatic wholesale loss in island‐mean coral cover occurred. Reductions in hard coral spatial clustering may therefore offer an early indication of the ecosystem becoming degraded prior to mass coral mortality. In contrast, the spatial clustering of competitive fleshy macroalgae remained unchanged through both bleaching events, while crustose coralline algae and fleshy turf algae became more spatially clustered at larger scales (200–700 m) following mass bleaching. Overall, benthic community spatial patterning became less predictable following bleaching and was no longer reflective of gradients in long‐term environmental drivers that typically structure these remote reefs. Our findings provide novel insights into how climate‐driven marine heatwaves can impact the spatial properties of coral reef communities over multiple scales.