Debate on the issue is in many ways the crux of the conflict between Israel and Palestine, which is backed by Arab leaders, including Saudi Arabia, and the wider Islamic world.
The Pope also said Trump's move could inflame the Muslim world.
U.S. President Donald Trump has made clear his intention to recognize Jerusalem as the capital of Israel and move the embassy there from its current position in Tel Aviv.
The pope spoke at the end of his weekly general audience December 6, the same day that Trump was expected to announce his decision to move the USA embassy to Jerusalem from Tel Aviv, fulfilling a promise he made during his presidential campaign.
Pope Francis says he can not remain silent about a White House plan to recognize Jerusalem as Israel's capital.
Weighing in on the controversial decision, the pontiff made a "heartfelt appeal" to all nations to "respect [Jerusalem's] status quo, in conformity with the pertinent United Nations resolutions", as cited by Vatican Radio.
Turkey's president Recep Tayyip Erdogan has warned to cut diplomatic ties with Israel if the United States recognises Jerusalem as its capital. In this regard, I can not remain silent about my deep concern for the situation that has developed in recent days and, at the same time, I wish to make heartfelt appeal to ensure that everyone is committed to respecting the status quo of the city, in accordance with the relevant Resolutions of the United Nations.
He said he hoped "wisdom and prudence prevail, in order to avoid adding new elements of tension to a global panorama that is already convulsed and marked by so many and cruel conflicts".
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In his general audience, Pope Francis noted how Jerusalem is a "unique city" that is considered holy for Jews, Christians and Muslims.
Pope Francis spoke to pilgrims in the Vatican's Paul VI Hall during his weekly general audience, during which he recounted the phases of his recent November 27-Dec.
"The primary condition of that dialogue is reciprocal respect and a commitment to strengthening that respect, for the sake of recognising the rights of all people, wherever they happen to be", he said.
Francis spoke by telephone Tuesday with Palestinian leader Mahmoud Abbas, after President Donald Trump told Abbas of his decision to recognize Jerusalem as Israel's capital.
In Bangladesh, a majority Muslim country, the pope's trip was aimed at fostering dialogue between Islam and Catholicism, following in the footsteps of the previous papal visits by Pope Paul VI and Saint John Paul II.
The Vatican said the call with Francis was made at Mr Abbas's initiative.
The Vatican signed its first treaty with the "State of Palestine" the following year.
This irked Israel because his predecessor had always gone first to Israel and entered the territories from Israel.