One of the main functions of zoos today is the breeding and reproduction of rare, endangered, and protected species of animals.

Sofia Zoo participates in the European Endangered Species Programme (EEP, EAZA Ex situ Programmes) of the European Association of Zoos and Aquariums (EAZA) with the following valuable animal species kept at the zoo, some of which are successfully breeding: jaguar, Persian leopard, striped hyena, snow leopard, white-handed gibbon, black and white colobus, lion macaque, Hanuman langur, Vietnamese sika deer, takin, addax antelope, dwarf hippopotamus, white rhinoceros, Asian elephant, Egyptian vulture, black vulture, sloth bear. EAZA Ex-situ programmes (EEP) are programmes for the management of populations of endangered animal species in captivity, which are managed by EAZA members. The aim of the EEP is to maintain populations of animals with preserved genetic diversity within the EAZA and beyond. Together with the Regional Plans for Regional Collection Plans and Long-term Management Plans, EEP are one of the pillars of the EAZA population management structure. EAZA currently manages programs for over 400 different species.

Sofia Zoo also participates in the European Stud Book (ESB) with the following species: Eurasian lynx, Eurasian brown bear, Himalayan bear, kinkajou, meerkat, lychee antelope, hippopotamus, red kangaroo, griffon vulture, grey-cheeked rhinoceros and box turtle. The European Stud Book is a form of management of species kept in European zoos. The staff responsible for the breeding of the species collect information on births, deaths, transfers from all zoos in the European Association of Zoos and Aquariums (EAZA). Based on the collected data, the ESB provides guidelines for optimal population management.