Mogherini noted that the global community, including the European Union and other U.S. allies, will continue to abide by the deal even if Trump chooses not to certify Iran's compliance, something which has been confirmed eight times by the worldwide Atomic Energy Agency (IAEA).
USA officials told CNN Trump was moving forward with his decision despite the assessment by the global community, which said Iran was maintaining its condtions under the Joint Comprehensive Plan of Action (JCPOA) agreement.
Iran has said it is open in principle to further discussions, particularly with Europe, but has said its missile programme is non-negotiable.
Under the 2015 deal, Tehran agreed to roll back its nuclear program in exchange for relief from wide-ranging oil, trade and financial sanctions that had choked the Iranian economy.
President Trump's upcoming decision on how he will deal with the unsafe and flawed nuclear agreement is a moment for moral clarity and may be a defining moment of his presidency.
Gen. Joseph Dunford, the chairman of the Joint Chiefs of Staff, told the Senate Armed Services Committee last week that Iran "is not in material breach of the agreement".
Even so, some experts told CNBC that decertification will undermine the worldwide deal and encourage hardliners in Tehran to push for nuclear weapons. That declaration could lead to an unraveling of the seven-nation pact and leave the United States, not Iran, as the country that balked at honoring its commitments.
In addition, Trump could at any time decide not to waive the nuclear-related sanctions again - a decision he must make every 120 days under USA law.
Drafts of two proposals seen by The Associated Press, one from Senate Foreign Relations Committee chairman Bob Corker and one from committee member and harsh deal critic Senator Tom Cotton, would expand the United States certification criteria to include items that are also the province of the UN nuclear watchdog and require the U.S. intelligence community to determine if Iran is carrying out illicit activity in facilities to which the International Atomic Energy Agency does not have access.More news: Isis 'White Widow' Sally Jones is killed by U.S. drone strike
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Under the dumb and dumber options being promoted by McMaster, Tillerson and other Trump advisers, this farcical situation will continue as the United States remains in the nuclear deal while engaging in pointless talks begging the Iranians for a better one.
"I expect President Trump will not certify it", said Elizabeth Rosenberg, an Iran expert at the Center for a New American Security, a progressive think tank. "Once it was entered into, once it was implemented, we want to see it enforced".
Watch Federica Mogherini's full interview with the NewsHour's Judy Woodruff on Wednesday.
The reversal underscores deep concerns among lawmakers that Trump will inform Congress in the coming days that the landmark 2015 agreement with Iran is contrary to America's national security interests.
But Iranian officials have already ruled out any renegotiation of the deal.
First, Congress could vote to snap sanctions back into place, or Trump could refuse to sign the next round of waivers for sanctions. But it is a requirement of US law. That could include Iran pulling out of the deal as well and restarting uranium enrichment activities, or Iran could stay in the deal and try to drive a wedge between the US and its allies.
Trump has threatened to scrap the agreement, calling it the "worst deal ever".
In this environment, many Democrats believe working on the periphery of the deal could be the congressional equivalent of destroying the village to save it.
The "we must avoid alienating European leaders" argument is unlikely to sway Mr. Trump since he proved by his decision to withdraw from the equally flawed Paris Climate Accord that he rightly believes Europe does not have a veto over USA foreign policy or his decisions as president. Congress would act under provisions of the Coker-Cardin Act which allow expedited consideration of taking such action over a 60-day period.