Debbie Cook had testified in a Texas court that she witnessed church leader David Miscavige physically punch another Scientology executive in the face at the church's international headquarters in Riverside County.
Cook also testified that she was held for seven weeks in a place called "The Hole," a set of double-wide trailers on that base.
Her explosive testimony came after the church filed suit against Cook in January for allegedly violating the confidentiality agreement she signed when she left the church in 2007. Cook countersued the church.
Scientology has denied all of Cook's allegations, calling her a "bitter, defrocked apostate." Details of the settlement are confidential.