Regular cooperative online community challenges focused on conservation (such as breeding and releasing as many giant pandas to the wild within a certain timeframe) allow players to receive 'conservation credits,' which can be redeemed for new animals instead of regular in-game currency. Animals can be purchased and traded with other players' zoos through an online marketplace. The franchise mode allows the player to build multiple franchise zoos with a shared economy and animals. The game features four modes: sandbox, career, challenge, and the online franchise mode.

The game features a dynamic day/night cycle, weather patterns, and animal poop physics. Safari, boat, train, monorail, and gondola lift rides can also be constructed throughout the zoo for transportation and to offer guests additional ways of viewing animals. Custom structures can be uploaded as ' blueprints' for other players to download for free and place in their own zoos via the Steam Workshop. By allowing these items to phase-into and/or lock with each other, the creative player can create elaborate buildings, landscaping, and natural structures such as waterfalls and cave systems from scratch. Like Planet Coaster, Planet Zoo provides over a thousand building pieces such as benches, lighting, flowers, trees, and items such as individual planks of wood, glass, rocks, and roof tiles. This includes hiring staff, constructing guest amenities and staff facilities, performing research, and working towards the conservation of threatened and endangered species. In addition to ensuring animal welfare, the player must deal with managing the park as an institution. As such, elements such as inbreeding may have negative consequences on progeny. Each animal has their own genome within the game's breeding system, which reflect its life expectancy, size, health, and fertility and can be passed down through offspring. Predators can attack and kill other animals, but unlike in Zoo Tycoon, cannot attack guests. Each species has its own requirements and needs that players must satisfy through creation of a suitable exhibit environment and adequate behavioral enrichment.

For instance, wolves adopt a pack mentality and animals of the African plains (such as elephants, giraffe, zebras, wildebeest, and buffalo) can live together in a single mixed-species habitat. Animals, controlled by artificial intelligence, behave similarly to their real-life counterparts.

Planet Zoo tasks players with building a zoo, with animal species in the base game and new species available through sixteen separate downloadable content packs and the Deluxe Edition.

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