The pontiff thanked those who received him at the Vatican embassy.
The pontiff is meeting with young people at the Morelos Stadium, in Morelia.
As many as 200,000 Catholics are expected to cross four bridges from El Paso, Texas into Ciudad Juárez, Mexico on Wednesday to see Pope Francis.
English16/02/2016
Pope Francis says mass in Morelia
The visit to Morelia is a tangible sign of Francis' respect for the city's archbishop, Alberto Suárez Inda, whom Francis made a cardinal last year.
The Pope spoke to the faithful surrounding the embassy and took some pictures with them.
Boston Cardinal Sean O'Malley went beyond the Vatican's guidelines for bishops.
He also prayed before the tomb of controversial Bishop Samuel Ruiz.
The four Díaz sisters and some male relatives played the instrument while people took communion.
About 100,000 gathered on the dirt field of a sports complex for the Mass in San Cristóbal de las Casas.
The visit, at the midway mark of Pope Francis' five-day trip to Mexico, is also aimed at boosting the faith in the least Catholic state in Mexico.