Yohannes acts harshly towards Europeans due to the violent religious controversy that Catholic missionaries had caused in Ethiopia under the reign of his grandfather Susenyos.

He convokes a church council in 1669 in Gondar, directing Gerazmach Mikael to expel all of the Catholics still living in Ethiopia; those who do not embrace the beliefs of the Ethiopian Church are exiled to Sennar.

His reign sees the execution of six Franciscans sent by Pope Alexander VII to succeed in converting Ethiopia to Catholicism where the Jesuits had failed thirty years before.

Yohannes favors Armenian visitors, whose beliefs also embrace Miaphysitism, and are in harmony with the Ethiopian Church.

These include one Murad, who undertakes a number of diplomatic missions for the Emperor.