The breeding season of Bonelli's eagles is from late January/February to July in the western part of the range and November-August/September (peaking December-May) in the Indian subcontinent and Myanmar. Both members of the pair may dwell around the eyrie for up to 2-3 months before breeding. Their nest is a huge structure of branches and sticks, scarcely smaller than those built by eagles twice the size of this species, though rarely as great in depth as some old nests of the larger eagles. Often the nest completely obscures the sitting female from view unless it is seen at the same level or higher than the nest. Nest size can average up to across and deep but with repeated use the nest can range up to in both directions (record sized nest in India was in height). Tree nests tend to average larger than those placed on cliff ledges. One nest in the Gir forest was used periodically used over the course of 30 years. While they may line their active nest with greenery, it is less frequent and sparser where present than in many other birds of prey. Nesting locales are often high on cliff ledge or at (usually over ) above the ground in large tree. Very rarely, nests may too be on the perimeter of buildings. The trees selected are often the tallest and/or most densely foliaged in a given stand. Their close cousin, the African hawk-eagle, usually nests on trees and rarely utilizes crags and alternate nesting sites as does the Bonelli's. Historically, throughout their range in western Europe, Bonelli's eagles were considered almost obligate cliff nesters on almost any rocky environment, from precipitous mountain ranges, canyons over river valleys, even down to low rocky rubble to sea cliffs. However, up to 52 tree nests for the species have now been recorded in southwest Portugal. Often the Portuguese nesting eagles used invasive Tasmanian blue gum (Eucalyptus globulus) (44.2% of the time) while a further 21.2% were on cork oak (Quercus suber) not to mention some that were placed on large shrubs, i.e. strawberry trees (Arbutus unedo). The mean height of Portuguese tree nest was . The Portuguese study further found 67.3% of the tree nests to be on hill slopes and average height for lowest branch, both presumably as anti-predator measure. By 2017, the expansion to using tree nests had bolstered the southwest Portugal population considerably. In the 1990s, the first ever tree nest was found in the relative Bonelli's eagle stronghold of Catalonia, Spain, while another singular tree nest was also found in the south of France. In India, Bonelli's eagles seem to readily switch between tree and cliff nests. The eagles of areas such as Maharashtra and the Western Ghats are usually partial to nesting in trees while in the Deccan Peninsula, Indo-Gangetic plain and Himalayan foothills, the eagles alternated between nesting on cliffs and lofty trees including red silk cotton (Bombax ceiba), sacred fig (Ficus religiosa), Javan plum (Syzygium cumini) or Dalbergia ssp. Bonelli's eagles in India may also nest close to human habitations if disturbance is low, such as in Saurashtra and in Himalayan foothills, in the latter often in large chir pine (Pinus roxburghii) near villages. In Pakistan, the species has been known to use seaside cliffs. Also, in the Indian desert zone, Bonelli's eagles are known to use relatively low rocky hills with shallow gradients, making the nest ledges relatively easy to access. On Cyprus, 70% of nests were in Turkish pines (Pinus brutia) at a mean elevation of . Often this eagle uses the same nest in successive years but also alternate nest may be used. Often somewhere between 1 and 5 nests may be built by the species on their home range. Like other birds of prey, the presence of alternate nest may be a strategy to cope with ectoparasitic infestations within the nest. The construction of a new nest takes roughly a month's time.