Trump is also expected to approve moving the USA embassy from Tel Aviv to Jerusalem, although not immediately.
"Jerusalem is a unique city, sacred for Jews, Christians and Muslims", he said, adding that it was home to sites deemed holy by followers of the three major monotheistic faiths.
Arab leaders have warned the Trump administration's decision would subvert decades of USA foreign policy and risk triggering further conflicts and violence in the Middle East.
"At the same time, I would like to make a heartfelt appeal for everyone's commitment to respect the city's status quo, in conformity with the pertinent United Nations Resolutions", he said.
The pope told thousands of people at his general audience: "I can not keep quiet about my deep worry about the situation that has been created in the last few days".
In his remarks, Pope Francis said the Holy Land was the "land par excellence of dialogue between God and mankind".
"I pray to the Lord that this identity may be preserved and strengthened for the benefit of the Middle East and of the entire world", Francis continued, "and that wisdom and prudence prevail, to avoid adding new elements of tension in an already convulsed worldwide panorama marked by so many cruel conflicts".
Jerusalem, the pope said, holds a "special vocation for peace".
To conclude, Pope Francis thanked the president of Palestine, Mahmoud Abbas, for his attention to Christian communities and wished peace upon Palestine and the whole Middle East.
He spoke of having open communication and holding talks between differing religions "and also in civil society".
The Pope made comments to a group of visiting Palestinians involved in inter-religious dialogue with the Vatican.
He added that Israel must not allow its own interests to "disrupt what the United Nations has repeated many times, and what has also been the logical and coherent position of the Holy See for all the past decades".
When Francis visited the Holy Land in 2014, he flew directly by helicopter from Jordan to what the Vatican programme called the "State of Palestine" and visited Israel last.
"They came to the Vatican with the intention of establishing a joint working group".
This irked Israel because his predecessor had always gone first to Israel and entered the territories from Israel.