Though Mary Tudor was a loyal Catholic, she was surrounded at court by numerous opponents of papal authority, who made it difficult for Commendone to obtain a secret interview with her.
Commendone continued to hold the office of papal secretary under Pope Paul IV, who esteemed him very highly and in return for his services appointed him bishop of Kephalonia and Zacynthus in 1555.
In the summer of 1556 he accompanied Cardinal Legate Scipione Rebiba on a papal mission to the Netherlands, to the courts of Charles V, Holy Roman Emperor and King Philip II of Spain, the consort of Queen Mary of England.
On 16 September of the same year the pope sent him as extraordinary legate to the Governments of Urbino, Ferrara, Venice, and Parma in order to obtain help against the Spanish troops who were occupying the Campagna and threatening Rome.
Leaving Berlin, Commendone visited Beeskow, Wolfenbüttel, Hanover, Hildesheim, Iburg, Paderborn, Cologne, Cleves, the Netherlands, and Aachen, inviting all the Estates he met in these places.
From Aachen he turned to Lübeck with the intention of crossing the sea to invite Kings Frederick II of Denmark and Eric XIV of Sweden.
In October of the same year Pius IV sent him as legate to King Sigismund II of Poland with instruction to induce this ruler to give political recognition to the Tridentine decrees.
While engaged in this mission, Commendone was also empowered by a papal Brief dated 10 October 1568, to make an apostolic visitation of the churches and monasteries of Germany and the adjacent provinces.
Upon his return to Italy in 1573, Pope Gregory XIII appointed him a member of the newly founded Congregatio Germanica, the purpose of which was to safeguard Catholic interests in Germany.