Recent concerns about the viability of zoo populations have motivated studies on the historic and current status of animal populations in North American and European zoos. However, these evaluations may not accurately reflect the populations’ long-term viability in the decades to come. Here, we assessed the projected future status of North American zoo populations by conducting standardized population viability analyses (PVAs) for 137 cooperative breeding programs. We summarized PVA results to describe patterns in viability across populations, and examined whether viability can be predicted by biological or management-based factors. Under recent management practices and without imports or exports of animals, 64% of populations will decline in size over the next 25 years, and only 18% would retain ≥90% of the founding gene diversity (GD) in 100 years. However, viability would improve if programs can implement management changes (e.g., increasing reproduction, increasing holding space, and importing genetically unique individuals, as appropriate): only 16% of populations would still decline in 25 years, and 49% would retain ≥90% GD in 100 years. Programs with more participating institutions and a “green” Association of Zoos and Aquariums animal program designation were projected to have higher metrics of demographic viability, and those with longer lifespans and lower recent death rates were projected to have higher metrics of genetic viability. Due to the large variation in species life history, management goals, and constraints across programs, our findings suggest there is unlikely to be a single path to long-term viability that would be appropriate for all zoo populations.