After the closing of the 1984 Louisiana World Exposition in New Orleans, the expo’s visitor monorails were moved to Florida to be re-purposed at Miami MetroZoo and operated until 2022.

In 1992, the zoo suffered extensive damage when Hurricane Andrew made landfall in South Florida, on August 24.

The small, yet intensely powerful category 5 hurricane toppled over 5,000 trees and destroyed the Wings of Asia aviary (which had been built to withstand winds of up to 120 miles per hour (193 km/h)) resulting in the loss of approximately 100 of the 300 resident birds.

[15] The Falcon Batchelor Komodo Dragon Encounter opened that same year, followed by exhibits featuring Andean condors (1999), meerkats (2000), Cuban crocodiles and squirrel monkeys (2001).

The rebuilt Wings of Asia aviary, housing more than 300 individual birds and representing 70 species, refurbished in the spring of 2003.

[24] Zoo Miami supports conservation programs at the local, national and global level, and was a founding member of the AZA's Butterfly Conservation Initiative (BFCI), a program designed to assemble governmental and non-governmental agencies to aid in the population recovery of vulnerable, threatened and endangered butterflies in North America.

[25] There are five main exhibit sections in the zoo: Florida: Mission Everglades, Asia, Africa, Amazon and Beyond, and Australia.

The zoo's main entry includes an entryway canopy structure, conjoining ticket booths and gift shop, and an adjacent American flamingo exhibit.

[27] Several species not native to Asia are also found in this area like African lions, African painted dogs, spotted hyenas, okapis, addax, sable antelope, addra gazelles, mongoose lemur, black crowned cranes, and Cuban crocodiles.

Both were separated during the storm, Seetna moved to Two Tails Ranch (Patricia Zerbini) and stayed there for breeding purposes but died of labor issues in 1996 while Dalip returned to Zoo Miami in 1995 where he remained until his death in 2022.

Visitors can observe species including reticulated giraffes, pygmy hippos, African bush elephants, eastern black rhinoceroses, greater kudus, nyalas, slender-horned gazelles, Grevy's zebras, giant elands, chimpanzees, western lowland gorillas, mountain bongo, yellow-backed duikers, okapis, and servals.

[34] Eleven-year-old "Pongo," at sixteen feet the tallest giraffe in the zoo, was euthanized on January 4, 2021, after failing to recover from a foot injury.

[35] Amazon and Beyond, situated in the zoo's northwest corner, opened on December 6, 2008, and is a collection of South America animals.

Three areas represent native habitats that are found in the Amazonian region—the "cloud forest", the Amazon River basin, and the Atlantic Forest-Pantanal—with species such as giant otters, jaguars, Orinoco crocodiles, giant anteaters, black howler monkeys, black-handed spider monkeys, Hoffmann's two-toed sloths, harpy eagles, fruit bats, poison dart frogs, and various Amazonian fish.

Situated near this to habitat, is the 800-seat Sami Family Amphitheater, where daily animal presentations, concerts and cultural events are held.

The amphitheater is named in memory of Albert and Winifred Sami, who anonymously donated an estimated $3 million to the zoo from 1993 until their deaths in 2007 and 2014, respectively.

[37] Zoo Miami recently celebrated the birth of a baby koala, who was actually born in May 2019, but only emerged from its mothers pouch on January 8, 2020.

[38] Near the Australian habitat is a trail with Galapagos giant tortoises, babirusas, red river hogs, common warthogs, and Visayan warty pigs.