Obama, a regular churchgoer, will participate in a discussion called "Engaged in shaping democracy - taking responsibility at home and in the world" on May 25th at Berlin's Brandenburg Gate.
It is part of this year's Kirchentag (Church Day), which runs from May 24th to 28th, and is expected to attract 140,000 visitors.
Co-hosted by the Obama Foundation and Germany's Evangelische Kirchentag (Protestant Church Day), the event will also feature Reverend Thabo Makgoba, the Anglican Archbishop of Cape Town.
This year's Church Day comes as Germany commemorates the 500th anniversary of the Reformation, a seismic theological shift started by Martin Luther who criticized the indulgences of the Catholic Church and challenged the authority of the Pope and place of the saints.
Luther's 95 theses, which he nailed to the door of a church in eastern Germany's Wittenberg in 1517, led to the split with the Catholic church and gave birth to Protestantism.
Obama visited Berlin in November as part of his last foreign tour before handing over to President Donald Trump.
It was also in the German capital where Obama held the biggest rally of his 2008 watershed campaign.
Although Merkel barred him from speaking at the Brandenburg Gate, Obama - then a senator - drew 200,000 cheering fans to the nearby Victory Column monument for a speech about ripping down walls of division.
He finally spoke at the Brandenburg Gate in 2013, to an audience of invited guests.
Obama and Merkel formed a strong bond over the course of his tenure, with Obama calling her his "closest international partner", and thanking her for "eight years of friendship" ahead of his departure from the White House.