The Blue-throated macaw was severely threatened in the past by illegal exploitation for the pet trade, this has been radically reduced since 2000. All known sites are on private cattle-ranches, where burning and clearing for pasture, and tree-felling for fuel have reduced the number of suitable nest trees and inhibited palm regeneration.

Nest-site competition from other macaws, toucans and large woodpeckers is significant. Indiscriminate hunting to provide feathers for indigenous head-dresses has had a small impact in some areas and small scale random hunting to provide meat for baiting fish hooks also occurs. There are fears that inbreeding within an increasingly fragmented population is resulting in reduced fertility.

Several breeding and conservation schemes in zoos have now been set up to save this species. Other projects have been started to protect the remaining wild population, but at present numbers are still decreasing.