The zoo sees its primary goal as the conservation of endangered species.
These include animals mentioned in the Bible which are now extinct in Israel, such as the Asian lion, the Syrian brown bear, the Asiatic cheetah, the Nile crocodile and the Persian fallow deer (which has been reintroduced in Israel), and the critically endangered Arabian leopard which is on the verge of extinction in Israel.
It also includes endangered species worldwide, such as the Asian elephant, rare species of macaw, the cockatiel, the ibis, and the golden lion tamarin.

Towards that end, the zoo undertakes to breed animals in captivity and, in some cases, reintroduce them to the wild.
Through this program, the zoo has successfully increased the number of Persian fallow deer in Israel.
This species was thought to be extinct in the 20th century until a small number of deer were located in Iran in 1956.
In 1978, four of these deer were brought to Israel and have since increased to several hundred, with a major breeding colony at the Jerusalem Biblical Zoo.
A concurrent project to protect the Negev tortoise from extinction involves breeding from artificially-incubated eggs.

There is a captive breeding programme for the blind cave shrimp Typhlocaris galilea.

At the zoo's National Center for Artificial Incubation of Raptor Eggs, eggs of raptors that are either extinct or severely decimated in Israel are incubated from captive-breeding pairs.
The griffon vulture, an endangered species, is the subject of much research activity.
The zoo has successfully mated vultures with crippled wings – a feat that ornithologists previously thought could not be accomplished because these birds could not balance themselves properly.
It has also used two male vultures to hatch and raise chicks from incubated eggs.
Additionally, the zoo participates in a countrywide breeding program coordinated by the Israel Nature and Parks Authority to increase the birth rate of griffon vultures in the wild.

The zoo conducts a small ceremony each time it returns a bird to the wild.
In 1996, for the release of a griffon vulture which it named "Freedom", the zoo invited the mother of captured Israeli navigator Ron Arad to help release the bird.

The zoo is considered a world leader and educator in reproductive intervention.
It achieved a major success in December 2005 with the birth of Gabi, the first elephant conceived in Israel through artificial insemination.
In conjunction with a team from the Reproduction Management Institute for Zoo Biology and Wildlife Research of Berlin, zoo veterinarians impregnated one of their female elephants, Tamar, with sperm obtained from Emmett, a bull elephant in the Whipsnade Animal Park, Bedfordshire, England.
On 10 December 2005, Gabi's six-hour birth was viewed by over 350,000 people in 108 countries via live streaming on the zoo's website.

The zoo has also pioneered the use of animal birth control.
It was the first to use a dart gun to implant a slow-release hormone into the thigh of a female giraffe; she is the daughter of the zoo's bull giraffe, and inbreeding is inadvisable.
The zoo uses slow-release hormones to control its chimpanzee and mandrill populations, which are reproducing too quickly for the space they occupy; letting the animals multiply and sending family members to other zoos is unwise, according to veterinarians.

Newborn animals that are threatened or ignored by their parents are raised by the veterinary staff.
On 31 December 2008, for example, a newborn tiger cub ignored by its mother was taken home by a staff member to be bottle-fed.
A newborn leopard rejected by its mother spent its days at the zoo and nights at veterinarians' homes for its first three and a half months of life.

The zoo also provides medical treatment for animals and birds injured in the wild.
The wildlife is either released back to their natural environment (if they are healthy enough) or placed in other zoos.
In the late 2000s, an aviary was built for eagle owls which the zoo is nursing back to health.
The zoo sees its primary goal as the conservation of endangered species. These include animals mentioned in the Bible which are now extinct in Israel, such as the Asian lion, the Syrian brown bear, the Asiatic cheetah, the Nile crocodile and the Persian fallow deer (which has been reintroduced in Israel), and the critically endangered Arabian leopard which is on the verge of extinction in Israel. It also includes endangered species worldwide, such as the Asian elephant, rare species of macaw, the cockatiel, the ibis, and the golden lion tamarin.
Towards that end, the zoo undertakes to breed animals in captivity and, in some cases, reintroduce them to the wild. Through this program, the zoo has successfully increased the number of Persian fallow deer in Israel. This species was thought to be extinct in the 20th century until a small number of deer were located in Iran in 1956. In 1978, four of these deer were brought to Israel and have since increased to several hundred, with a major breeding colony at the Jerusalem Biblical Zoo. A concurrent project to protect the Negev tortoise from extinction involves breeding from artificially-incubated eggs.
There is a captive breeding programme for the blind cave shrimp Typhlocaris galilea.
At the zoo's National Center for Artificial Incubation of Raptor Eggs, eggs of raptors that are either extinct or severely decimated in Israel are incubated from captive-breeding pairs. The griffon vulture, an endangered species, is the subject of much research activity. The zoo has successfully mated vultures with crippled wings – a feat that ornithologists previously thought could not be accomplished because these birds could not balance themselves properly. It has also used two male vultures to hatch and raise chicks from incubated eggs. Additionally, the zoo participates in a countrywide breeding program coordinated by the Israel Nature and Parks Authority to increase the birth rate of griffon vultures in the wild.
The zoo conducts a small ceremony each time it returns a bird to the wild. In 1996, for the release of a griffon vulture which it named "Freedom", the zoo invited the mother of captured Israeli navigator Ron Arad to help release the bird.
The zoo is considered a world leader and educator in reproductive intervention. It achieved a major success in December 2005 with the birth of Gabi, the first elephant conceived in Israel through artificial insemination. In conjunction with a team from the Reproduction Management Institute for Zoo Biology and Wildlife Research of Berlin, zoo veterinarians impregnated one of their female elephants, Tamar, with sperm obtained from Emmett, a bull elephant in the Whipsnade Animal Park, Bedfordshire, England. On 10 December 2005, Gabi's six-hour birth was viewed by over 350,000 people in 108 countries via live streaming on the zoo's website.
The zoo has also pioneered the use of animal birth control. It was the first to use a dart gun to implant a slow-release hormone into the thigh of a female giraffe; she is the daughter of the zoo's bull giraffe, and inbreeding is inadvisable. The zoo uses slow-release hormones to control its chimpanzee and mandrill populations, which are reproducing too quickly for the space they occupy; letting the animals multiply and sending family members to other zoos is unwise, according to veterinarians.
Newborn animals that are threatened or ignored by their parents are raised by the veterinary staff. On 31 December 2008, for example, a newborn tiger cub ignored by its mother was taken home by a staff member to be bottle-fed. A newborn leopard rejected by its mother spent its days at the zoo and nights at veterinarians' homes for its first three and a half months of life.
The zoo also provides medical treatment for animals and birds injured in the wild. The wildlife is either released back to their natural environment (if they are healthy enough) or placed in other zoos. In the late 2000s, an aviary was built for eagle owls which the zoo is nursing back to health.
Jerusalem Biblical Zoo