"Immigration is a privilege, not a right, and the safety of our citizens must always come first, without question", Trump said in the wake of court rulings blocking his second attempt to temporarily ban refugees as well as travellers from six Muslim-majority nations.
He said Germany must stump up more money to the U.S. in order to cover the cost of the defence it provides.
The two were left to talk, based on the premise that, in Merkel's words, "it's much better to speak with each other than past each other".
Trump on Friday said he had "reiterated to Chancellor Merkel my strong support for North Atlantic Treaty Organisation, as well as the need for our North Atlantic Treaty Organisation allies to pay their fair share for the cost of defense".
Among other revelations, former National Security Agency contractor Edward Snowden exposed the agency's monitoring of Merkel's phone under former President Barack Obama - creating one of the worst rifts in German-American relations since the country was united after the Cold War.
"I thanked the chancellor for her commitment to spending 2% of GDP [on NATO]", said Trump, adding that he fully supports North Atlantic Treaty Organisation.
"We need to be fair with each other", said Mrs Merkel, saying both countries were expecting "that something good comes out of it for their own people".
It is unclear whether or not Trump heard the chancellor, but clips of the exchange immediately made the rounds on Twitter. That's no surprise, as Trump has previously called Merkel a "catastrophic leader" and accused her of "ruining Germany", according to the Washington Post.
United Kingdom prime minister doesn't back second Scottish independence vote
Mrs May has accused the SNP of forcing a "fundamentally unfair" independence referendum that would damage Brexit negotiations. Instead, the First Minister has a plan which rests on winning public support for her position.
When the topic moved to trade, Trump said the US would do "fantastically well" in its trade relations with Germany.
Which is to say: The president of the United States just argued that it's perfectly appropriate for the White House to spread conspiracy theories that implicate close allies - so long as a 9/11 truther on Fox News spread them first. The president was slightly smiling when he said what he's got in common with Merkel.
"I don't believe in an isolationist policy, but I also believe that a policy of trade should be a fair policy", Trump said.
During a joint press conference, Trump was asked by a German reporter about his recent allegations that his predecessor spied on him during last year's allegations.
Comments like that have prompted some of Trump´s fiercest critics to declare Merkel the new "leader of the free world"-a moniker normally taken up by the occupant of the White House".
Those differences also are evident on trade, with Germans leading European opposition to a border-adjustment tax plan supported by US House Republican leaders that would make imports to the US more expensive.
Both German journalists asked about it point-blank.
"So you shouldn't be talking to me, you should be talking to Fox", he said. Exit question one: If it's true that Geert Wilders was damaged by comparisons to Trump, will Trump's antagonism inadvertently end up helping Merkel in this fall's elections?