He was made pope on 2 January 533. The basilica of Saint Clement still retains several memorials of "Johannes surnamed Mercurius". Presbyter Mercurius is found on a fragment of an ancient ciborium, and several of the marble slabs which enclose the schola cantorum bear upon them, in the style of the sixth century, the monogram of Johannes.
Mercurius was the first pope to adopt a new name upon elevation to the papacy.
At this period, simony (the purchase or sale of church offices or preferment) in the election of popes and bishops was rife among clergy and laity. During the sede vacante of over two months, "shameless trafficking in sacred things was indulged in.
Even sacred vessels were exposed for sale". The matter had been brought before the Senate, and laid before the Arian Ostrogothic Court at Ravenna.
The last decree (Senatus consultum) which the Roman Senate is known to have issued, passed under Boniface II, was directed against simony in papal elections.
The decree was confirmed by Athalaric, king of the Ostrogoths. He ordered it to be engraved on marble and to be placed in the atrium of Saint Peter"s Basilica in 533. By one of Athalaric"s own additions to the decree, it was decided that if a disputed election was carried before the Gothic officials of Ravenna by the Roman clergy and people, three thousand solidi would have to be paid into court.
This sum was to be given to the poor.
John remained on good terms with Athalaric, who, being an Arian Christian, was content to refer to John"s tribunal all actions brought against the Roman clergy. The notorious adulterous behavior of Contumeliosus, Bishop of Riez in Provence, caused John to order the bishops of Gaul to confine him in a monastery.
Until a new bishop could be appointed, he bade the clergy of Riez obey the Bishop of Arles. The answer to their question was given by Agapetus, as John II died on 8 May 535.
He was buried in Street Peter"s Basilica.