Most attention on tropical biodiversity conservation has focussed on protected areas. Recognising and enhancing the value of biodiversity outside, as well as inside, protected areas is increasingly important given recognition that biodiversity targets will not be met through protected areas alone. We investigated the extent to which protection influences colony occupancy and colony size of a species of conservation concern, the rock-nesting White-necked Picathartes Picathartes gymnocephalus. We used mixed models to compare long term trends at 42 colonies located both inside and outside a protected area of forest, Gola Rainforest National Park, and considered colonies further inside the boundary as being better protected. Colony occupation was primarily predicted by the level of protection, with occupation highest within protected areas, but was not different between colonies situated close to or far from the boundary. Mean colony occupation was consistently high in protected areas, and lower in unprotected areas. The surface area of colony rocks was also an important predictor with larger rock faces having a higher probability of occupancy. Our best models also included distance to forested habitat, presence of cleared forest and evidence of hunting as less important predictors. Over the eight-year study, after controlling for rock surface area, active colony size declined significantly. However, declines were only significant in colonies in unprotected forest, whilst colonies located within protected areas were buffered from significant decline. Together this suggests colony occupancy and the number of active nests are influenced by protection and human disturbance. Although a lack of demographic and population dynamic work on picathartes prevents identifying mechanisms, we show that despite unprotected colonies having lower occupancy and fewer active nests they can persist in human altered and disturbed areas, partly because larger traditionally used rocks remain important nesting sites.