Francis is the first pontiff to visit the North African country since John Paul II in 1985, and his arrival drew thousands to the streets on Saturday.
The Argentine was welcomed to Morocco by King Mohammed VI who describes himself as "commander of the faithful".
Speaking at Saturday's welcome ceremony, the pope defended "freedom of conscience" and "religious freedom".
Around 30,000 to 35,000 Catholics live in Morocco, many of them from sub-Saharan Africa.
Although Islam is the state religion, Moroccan authorities are keen to stress the country's "religious tolerance" which allows Christians and Jews to worship freely.
In a joint statement released by the Vatican on Saturday, the Pope and the King addressed the "sacred character of Jerusalem" saying the city should be a "symbol of peaceful coexistence" for Christians, Jews and Muslims.
Francis's palace meeting with the king was followed by a visit to an institute which hosts around 1,300 trainee imams and preachers.
Plight of migrants
While visiting a charity, the pontiff also highlighted the suffering of migrants, denouncing "indifference and silence" while calling on people to consider them "as people, not numbers".
Francis described Morocco as a "natural bridge between Africa and Europe" and said world problems could never be solved by “raising barriers” or "fomenting fear of others."
He criticised "collective expulsions" and said ways for migrants to regularise their status should be encouraged.
Morocco says it has a "humanistic" approach to migration and rejects allegations by rights groups of "brutal arrest campaigns" and "forced displacement" to the country's southern border.
The number of people taking the sea route from Morocco to Spain has recently surged as it has become harder for them to pass through Libya.