Eleonora’s Falcon is the commonest bird of prey in Greece, with more than 80% of the global population breeding on Greek islands. The aim of this study was to assess the population status and the colony characteristics for the species in the National Marine Park of Alonissos—Northern Sporades. Every island was circumnavigated twice in order to count individual birds and active nests during the breeding season of the species in 2021 by boat. Colony characteristics including nest category, nest height above sea level and nest orientation were recorded. The species was recorded nesting in 13 (12 uninhabited and 1 inhabited) out of 29 islands involving a total of 329 active nests. Most nests were in cliff cavities located between 12 m and 400 m above sea level, and had predominantly north-westerly and westerly orientations. These findings may inform conservation management decisions including minimization of disturbance in colonies, safeguarding colonies under threats, eradicating invasive species and protecting and enhancing the breeding habitat of the species in the specially protected area of the National Marine Park of Alonissos—Northern Sporades.