In Tallinn, the pontiff will meet with Estonian President Kersti Kaljulaid and will deliver a speech to the authorities and representatives of civil society.
The Holy Father will also take part in an ecumenical youth meeting in the Lutheran Saint Charles' Church before meeting with those assisted by the charitable organizations funded by the Church in the Cathedral of Saints Peter and Paul.
The pope's visit to Estonia will culminate with Holy Mass in Freedom Square.
Estonia is one of the least religious nations in the world, with the number of Catholics in the country put at 4,500, which accounts for less than 1 percent of the population.
The pontiff will fly back to Rome on Tuesday evening after ending his four-day Baltic tour in Estonia.