Photios had soon come into conflict with Pope Nicholas, who continues to refuse to recognize Photios as patriarch of Constantinople because his predecessor had been illegally deposed.

Nicholas, eager both to extend the growing power of the papacy over the empire and interested in the jurisdiction over the Bulgarians, who Photios has converted, in 863 orders the reinstatement of Ignatios.

The conflict, purely administrative at the beginning, acquires doctrinal undertones when Frankish missionaries in Bulgaria, acting as the pope's emissaries, begin to introduce an interpolated text of the Nicene Creed.

In the original text, the Holy Spirit was said to have proceeded "from the Father," whereas in Carolingian Europe (but not yet in Rome) the text has been revised to say "from the Father and the Son" (“filioque”).

Because Michael refuses to depose Photios, a schism with Rome results.

When Nicholas anathematizes and deposes Photios, the latter replies with a counter-excommunication.