However Pope Innocent III clearly stated that John was of Hungarian origin ("[...] quae de regno Hungariae originem duceret [...]"), when transferred him from Kalocsa to Esztergom in his papal bull of 6 October 1205, as Nándor Knauz's Monumenta ecclesiae Strigoniensis published the letter.

In the same year, John was a member of that papal committee, which investigated the charges against Elvin, Bishop of Várad, who was accused of simony and act of offense by the local chapter.

[5] When Emeric prepared a crusade under the pressure of Innocent in the spring of 1201, the pope sent a letter to Duke Andrew, Saul Győr, Archbishop of Kalocsa and John to "put aside the hostility and keep the peace of the realm" (i.e. govern the kingdom under the king's absence).

[9] To avert the Hungarian attack, Ban Kulin of Bosnia held a public assembly on 8 April 1203 and affirmed his loyalty to Rome in the presence of papal legate John de Casamaris, while the faithful abjured their mistakes and committed to following the Roman Catholic doctrine.

Following that King Emeric and Archbishop John held talks with Ban Kulin's unidentified son, the "heretic" envoys (priests Ljubin and Dragota) and the papal representative at Csepel Island.

In 1205, John sought to merge the "heretic" diocese in the "land of the sons of knez Belo" to the Roman Catholic Church, which laid south of the archbishopric (possibly in Serbia at the border).

Nevertheless, the papal policy remained inefficient, and later the autocephalous Serbian Orthodox Church emerged by 1219, under the influence of Stefan the First-Crowned and his brother Saint Sava, its first archbishop.

It appears that John tried to take advantage of the situation that Emeric's relationship with Job, Archbishop of Esztergom has deteriorated drastically, most likely because he remained neutral in the power struggle between the king and his younger brother, and stayed away from the secular affairs.

Under the pretext of Bogomilism along the southern boundary, Job requested Pope Innocent to receive a mandate of apostolic legate regarding the territory of the whole kingdom (i.e. also the Archdiocese of Kalocsa), when personally visited the Roman Curia in Palestrina (or Praeneste).

In April 1205, the pope sent a letter to John, who became de facto head of the Church in Hungary, and other prelates to support Ladislaus and his mother Queen Constance of Aragon.

[16] The dispute over the fill the position of Archbishop of Esztergom became a precedential event in the legal history of the Church, as the case and the following papal decretal ("Bone Memorie") appears among the glosses in English canonist Lawrence Somercotes' Tractatus.

The delegation consisted of the provost of Pressburg, the treasurer of Esztergom and two royal envoys – the abbot of Bakonybél and magister Peter (possibly identical with chronicler Anonymus), to strengthen John's position and emphasize the friendly relationship between him and Emeric.

Andrew immediately sent a letter with discourteous tone to the pope to inform him about developments and to promise that he will continue Emeric's launched measures, including the support of John's candidacy.

[21] The pope was infuriated by the fact that John had celebrated the coronation of Ladislaus III, violating the privileges of Esztergom (which also strengthened the arguments of the canons' representatives).

[23] Upon hearing of the pope's decision, some members of the Cathedral Chapter of Esztergom gathered and withdrew their support from John, who also lost his strongest promoter, King Emeric.

In his letter to the chapter (22 June 1205), Innocent ordered the canons to elect or unanimously nominate their archbishop within a month, and obtain the support of the suffragan bishops too, "if it is required" in Hungary.

[7] The case of John's election became part of the 13th-century decretal collections through Compilatio tertia (contains the documents of the first twelve years of the pontificate of Innocent III) and Liber extra.

On 12 February 1212, Innocent issued a bull dedicated to Andrew, John and the chapter, in which he refused to countersign the document, referring to its "harmful consequences" for the Kingdom of Hungary.

The pope also rejected the intention of Andrew to create a suffragan diocese of Szeben (today Sibiu, Romania) under the supervision of Berthold to the place of the eponymous provostry, which administratively affiliated to the Archdiocese of Esztergom.

[32] Nevertheless, John had several conflicts of jurisdiction with Berthold in the following years (for instance, in 1215, according to a letter from Pope Innocent),[33] who left Hungary only in 1218, when he was appointed as Patriarch of Aquileia.

After Robert's personal visit in Rome, the pope sent two legates, cardinals Pelagio Galvani and Stefano di Ceccano to Hungary in order to investigate the complaint and confirmed the privilege of the See of Veszprém in April 1216.

[36] In addition to the Hungarian lords, his "new institutions" altered the relations between the royal court and the prelacy, whose secular influence has decreased due to the increasingly enormous wealth of the laic power sphere.

Andrew granted large domains to her brother Bishop Egbert in the Szepesség region (now Spiš, Slovakia), while Berthold was made Ban of Croatia and Dalmatia in 1209.

When the king departed for a new campaign against Galicia in summer 1213,[40] taking advantage of his absence, Hungarian lords who were aggrieved at Queen Gertrude's favoritism towards her German entourage captured and murdered her and many of her courtiers in the Pilis Hills on 28 September.

[41] These works unanimously note John's famous phrase in his letter to Hungarian nobles planning the assassination of Gertrude: "Reginam occidere nolite timere bonum est si omnes consentiunt ego non contradico", can be roughly translated into "Kill Queen you must not fear will be good if all agree I do not oppose".

It is possible that Boncompagno heard the story in the Roman Curia and incorporated it into his rhetoric dissertation and textbook (published in 1235, the first written source of John's alleged letter).

[47] According to Andrew's letter, John was obedient to morality rather than rebelled lords' demands and "wickedness", thus he was imprisoned and exiled "in the midst of great injustice and shame", while his wealth was confiscated by "these tyrants".

[48] As compensation, Andrew donated the vineyards of Pográny (today Pohranice, Slovakia) and other landholdings (for instance, Gamás, Kapoly and Lulla) in Somogy County to John in 1218.

[49] It is possible that John was present in England on 7 July 1220, when Thomas Becket's remains were moved from his first tomb to a shrine, in the recently completed Trinity Chapel.

The event was attended by King Henry III, the papal legate Pandulf Verraccio, the Archbishop of Canterbury Stephen Langton and large numbers of dignitaries and magnates secular and ecclesiastical throughout from Europe.