CARMEN DEL EMERO, Bolivia — In this remote indigenous village in Bolivia, the rule has been the same for generations: Leaders can be re-elected only once. After that, they must hand power to someone else.

So it came as a shock to Nelo Yarari, the leader of Carmen del Emero, a community of indigenous Tacana people in the Bolivian Amazon, when President Evo Morales said he would be running for a fourth term.

Bolivia’s Constitution barred him from doing so, and Mr. Morales lost a referendum two years ago that would have allowed him to run again. Instead of giving up, he leaned on the courts, which then threw out the country’s term limits.

One thing especially stung for Mr. Yarari: As Bolivia’s first indigenous leader, Mr. Morales had vowed to champion native values from the presidential palace.