Under the sweeping, multi-decade initiative, dubbed "Operation Protect Catalina Island," deer would then be harvested and used as meat for the California Condor Recovery Program, helping provide a natural food source for the endangered birds, the nonprofit said.
It remains unclear exactly how many deer will be removed, as populations fluctuate between 500 and 1,800, according to the Conservancy.
The invasive deer, introduced in the early 1930s, "have no natural predators, so their population goes through extreme boom and bust cycles," the Conservancy said.
Over the years, they have reportedly decimated native vegetation, contributing to soil erosion, water loss, increased wildfire risks and reduced resources for native species.
"The evidence of the severity of the threat the deer pose is overwhelming, and all other alternatives have been exhausted," Scott Morrison, director of conservation and science for The Nature Conservancy in California, said in a statement. "Catalina Island can have either a functional, biodiverse and resilient ecosystem or it can have deer. It cannot have both."
The organization said the initiative will also include reintroducing native, fire-resistant plant species as officials seek to reduce escalating wildfire risks on the island.
It remains unclear when the plan to remove the deer will be implemented.