The Turkish leader urged the bloc to "keep its promises".
Turkey last month sent troops into neighbouring Syria to attack Kurdish YPG fighters near its southern border. This has added a further complication for the United States military campaign against Islamic State.
It was all smiles inside the Vatican when Turkish President Recep Tayyip Erdoğan met with Pope Francis on Monday morning. "We pray that you and the Turkish armed forces will achieve success and that Operation Olive Branch will. bring peace to the area", he wrote in a letter published by Turkey's Hurriyet daily.
Erdogan, in his visit to nthe Vatican, was accompanied by his wife and daughter and five ministers in a delegation that numbers 20 in all.
Jerusalem is home to sites holy to the Muslim, Jewish and Christian religions, and Trump's recent announcement that he would move the US embassy to the city alarmed many allies, who say the decision could doom Middle East peace efforts.
Speaking to reporters at Istanbul's airport prior to his departure for Rome, Erdogan said his visit to the Vatican to see the Pope - the first by a Turkish president in 59 years - was "a significant opportunity to draw attention to common human values". There were also reports of scuffles with the police.
Aided by interpreters, Pope Francis and Erdogan also focused on "the situation in the Middle East, with particular reference to the status of Jerusalem, highlighting the need to promote peace and stability in the region through dialogue and negotiation, with respect for human rights and worldwide law". However, as earlier reported, Erdogan planned to discuss the status of Jerusalem.
Jerusalem's status is perhaps the most sensitive issue in the Israeli-Palestinian conflict.
Anadolu Agency, a state-run Turkish news agency, said Erdogan and Francis also expressed the need to avoid "provocative statements that link Islam with terrorism".
Last week, Hebrew media reported that the US State Department, having already frozen some $100 million in UNRWA funding, was considering stopping all of its $360-million annual funding for the organization, and instead allocating it to other United Nations bodies that work with the Palestinians. "[It is] a symbol of a world based on peace and justice", the pope told Erdoğan as he gave him the medallion, made by the Italian artist Guido Verol. Several also held signs calling for the release of Abdullah Öcalan, a Kurdish nationalist leader who has been jailed in Turkey since 1999. Anti-migrant and Euroskeptic League leader Matteo Salvini said Monday he was "ashamed" that Italy was hosting a visit by Erdogan.