Obama, a regular churchgoer, will participate in a discussion called "Engaged in shaping democracy -- taking responsibility at home and in the world" on May 25 at Berlin's Brandenburg Gate.
It is part of this year's Kirchentag (Church Day), which runs from May 24 to 28, 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.
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.
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Obama, who developed a close working relationship with Merkel during eight years in the Oval Office, visited Berlin in November as part of his last foreign tour before handing over to President Donald Trump.
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.
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