At an airport welcoming ceremony with President Evo Morales by his side, Francis also praised Bolivia for taking "important steps" to include the poor and marginalised in the political and economic life of the country, South America's poorest.
The pontiff is on the second leg of his South American tour which started in Ecuador and finishes in Paraguay.
On his arrival to Bolivia he was greeted by a hug from the President who hung a pouch around his neck of woven of alpaca with indigenous trimmings. It's normally used to hold coca leaves which are chewed by local people to alleviate altitude sickness and have small levels of cocaine in. It's unknown whether Pope Francis chewed any leaves.
In his speech, Francis noted the Catholic faith took "deep root" in Bolivia centuries ago "and has continued to shed its light upon society, contributing to the development of the nation and shaping its culture".
"The voice of the bishops, which must be prophetic, speaks to society in the name of the church, our mother, from her preferential, evangelical option for the poor," he said.
The Pope is expected to raise environmental concerns during his Bolivian trip, just as he did in Ecuador.
As part of his trip he will visit the notoriously violent Palmasola prison where inmates largely control the inside.