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The development of commercial forests presents potential threats to large raptors that rely on prey caught in open country. We examined the effect of afforestation of breeding habitat used by a population of Golden Eagles Aquila chrysaetos in Scotland where, over the last 50 years, extensive stands of exotic conifers have been planted. Using data for 31 years on territory occupancy and breeding success, together with spatiotemporally dynamic mapping of forest cover and predicted areas of territory‐use in a Geographical Information System, we examined relationships between forest cover and Eagle ecology at landscape and individual territory scales. Several territories were abandoned during the earliest phases of forest planting, but relatively few were apparently lost to later plantings. Territories with poorer breeding productivity appeared to be more vulnerable to abandonment than territories with better breeding productivity. At the landscape scale, temporal differences in breeding productivity were negatively related to the extent of forest cover, although productivity of individual territories showed no clear relationship with forest cover. Several territories with less than a 5% increase in forest cover experienced reduced productivity; however, territories least constrained by neighbouring pairs of Eagles showed an increase in productivity. Territories experiencing the greatest increases in forest cover showed a greater use of spatially separated nest‐sites by occupying pairs. Hence, pairs that were less constrained by neighbours appeared to compensate for loss of open habitat by shifting their territory‐use, whereas pairs that were more constrained could not compensate for open habitat loss and suffered reduced productivity (and, probably in some cases, abandoned the territory). We suggest that simple guidelines based on the extent and locations of habitat loss are inadequate when predicting effects on large territorial raptors such as Golden Eagles. Consideration should also be given to the ‘quality’ of a territory or occupying pair, as well as the extent to which territory‐use is constrained by neighbouring pairs or other ‘unsuitable habitat’ which may have been affected by previous episodes of open habitat loss.