The New York City Department of Parks and Recreation contracted Wildlife Conservation Society to operate the zoo in 1988.

[14] That March, Mayor Robert F. Wagner Jr. requested that the New York City Council revise the City Administrative Code to permit the zoo's construction,[14] and New York state legislators introduced bills to allow the Queens Botanical Garden Society to operate the zoo.

[24] By that July, the city government was planning to construct the zoo on the site of the fair's former transportation area, west of the Grand Central Parkway, rather than next to the Queens Botanical Garden.

[25] Later that year, the TBTA announced more detailed plans for the zoo, which included a concession building and an aviary within the fair's geodesic dome.

[37] In addition, the zoo frequently experienced blackouts,[37][38] as the park's underground electrical ducts ran through marshland.

[47] As part of a planned United States Bicentennial celebration at Flushing Meadows–Corona Park, there were proposals to renovate the zoo.

Additional policemen were stationed in the surrounding area, and the zoo began employing curatorial staff 24 hours a day.

[57][58] City parks commissioner Edwin L. Weisl also supported the takeover,[59] and he preferred that the zoos be closed if the Zoological Society could not take over operations.

[74] Further contributing to its unpopularity, the Flushing Meadows Zoo closed at 4 p.m. each day, and the city government was not planning any major renovations.

[78][79] As part of the takeover, the Society planned to implement an admission fee, and it would spend $4.5 million renovating the zoo and adding animals.

[78] Queens borough president Donald Manes requested that the city provide $2 million for the zoo's renovation in its budget for fiscal year 1981.

[80] Negotiations continued for another year and a half, and the New York City Council and Board of Estimate had to approve the admission fees as well.

[99] The Zoological Society began drawing up plans for the zoo in 1986;[100] the renovation was part of a larger project to refurbish Flushing Meadows–Corona Park.

[110] The Flushing Meadows Zoo was temporarily closed for renovations on August 8, 1988,[111] and workers began razing the existing structures.

[114][115] Weeds started to grow in the zoo due to a lack of maintenance,[116] and the Zoological Society hired security guards to patrol the site.

[118] Mayor David Dinkins ultimately agreed to provide funding for the zoo after Queens borough president Claire Shulman threatened to prevent the nearby USTA National Tennis Center from being expanded.

[127] People frequently dumped unwanted animals at the zoo after it reopened, particularly during Easter, prompting objections from WCS officials.

[136] Following the September 11 attacks later that year, the zoo recorded increased attendance, in part because local residents were no longer traveling far.

[149] That June, the city government ultimately agreed to restore $4.8 million for the Prospect Park and Queens zoos,[150] though the WCS had to fire staff, discontinue programs, and double admission fees.

[161] In addition, borough president Melinda Katz provided $480,000 for renovations to the aviary and the overpass over the zoo's marsh.

[162] In March 2020, the Queens Zoo and the WCS's other facilities were shuttered indefinitely due to the COVID-19 pandemic in New York City.

[117][178] The wolves were removed,[122] and new exhibits were added for bears, bison, bobcats, coyotes, mountain lions, prairie dogs, Roosevelt elk, sandhill cranes, and water birds.

[122][179] The habitats include hidden landscape features, such as artificially warmed rocks in the mountain-lion exhibit, as well as tree stumps with sprinklers in the bison range.

[131] To mimic the conditions found in the wild, zookeepers hide food in landscape features such as tree trunks and logs.

[172] It consists of a geodesic dome designed by Thomas C. Howard for the 1964 fair,[182] based on a concept by Buckminster Fuller.

[178] The dome was originally located on what is now the site of the Buzz Vollmer Playground in the northern section of Flushing Meadows–Corona Park.

[22][26] According to park commissioner August Heckscher, the zoo could keep only North American animals because it operated throughout the year and because all the exhibits were outdoors.

[211] When the zoo opened, a reviewer for the New York Daily News said that "the city's latest animal farm is small...and beautiful".

"[120] Another Times writer, Dulcie Leimbach, described the zoo as "a comfortable yet exotic visit" and likened the landscape to a wooded backyard.

[178] A New York Daily News reporter wrote in 1996 that "you're sure to feel at home on this range" because of the zoo's activities and animals.