The main threat to the juveniles and adults of this species is the electrocution and collision with power lines, originating high mortality rates.

The abandonment of the traditional agricultural techniques, linked to the profound alteration on the habitat and landscape, affects the abundance of prey species, reducing the trophic resources available. This fact is aggravated by the occurrence of some diseases (like the Myxomatosis and the Viral Hemorrhagic Disease) and the cynegetic over-exploitation of prey populations, specially the European wild rabbit.

Direct persecution to this species still occur affecting mature and juvenile individuals.

The opening of new roads and the construction of big infrastructures in the breeding areas may constitute major disturbance factors affecting direct or indirectly the breeding success of this species.

The increase of the number of Bonelli’s eagle’s nests occupied by other species like Griffon vultures Gyps fulvus or Golden eagles Aquila chrysaetos may be a considerable threatening factor, especially when the couples are less stable or have reduced trophic resources.