Speaking during a joint press conference with U.S. Secretary of State Rex Tillerson, Mogherini said, "We believe that any action that would undermine this effort must absolutely be avoided... and that a solution has to be found for Jerusalem to be the capital of the two states".
In remarks to the press on the sidelines of the meetings, Germany's acting foreign minister, Sigmar Gabriel, said any unilateral U.S. recognition of Jerusalem as Israel's capital would inflame Middle East tensions.
Mogherini said, "The focus should therefore remain on the efforts to restart the peace process and avoiding any action that would undermine such efforts".
Trump is expected to formally acknowledge Jerusalem as Israel's capital on Wednesday, despite warnings from political leaders in Arab and Muslim-majority countries, who have said that doing so could prompt upheaval in the region.
Any decision by the U.S.to recognize Jerusalem as Israel's capital would be rife with political peril.
Fears that Trump might finally move on the sensitive issue and move the USA embassy to Jerusalem, effectively recognizing it as Israel's capital escalated last week.
"This step, if taken, will be in contradiction of the principle of not affecting final status negotiations, and contradicts worldwide resolutions that emphasize the historical and firm rights of the Palestinian people regarding Jerusalem", said the Ministry of Foreign Affairs in a statement.
Under the 1995 Jerusalem Embassy Act, the USA must move its embassy in Israel to Jerusalem, though the president can sign a waiver keeping it in Tel Aviv - a tradition that each president has followed.
She said the European Union and its member states would "continue to respect the worldwide consensus on Jerusalem embodied in, inter alia, UNSCR 478, including on the location of their diplomatic representations until the final status of Jerusalem is resolved".