During a visit to the Vatican, he noted that coca has been used for thousands of years as a medicinal cure in the Andes.
"I take it and I'm doing very well on it. I recommend that you take it, it will help sustain you," Morales told the pontiff.
The Holy Father sampled a tea made from coca leaves to combat altitude sickness on a visit to La Paz last year.
The Bolivian president, a long-time leader of a coca growers' union, spent half an hour with Francis discussing "current socio-economic conditions" among other issues, the Vatican said in a statement.
After they accused the Bolivian government of being involved in drug trafficking, the bishops were summoned by the president to provide a list of those involved.
Exchanging gifts, Morales offered the pope three books on the health benefits of the coca leaf.
The meeting was the third time the pope and Morales had met.
