"We have a MASSIVE trade deficit with Germany, plus they pay FAR LESS than they should on NATO & military. Very bad for US. This will change," Trump wrote in his tweet.
The fight has had few obvious practical consequences so far. But Merkel's meetings this week - first a chummy meeting with India's leader and then a sit-down with the Chinese Prime Minister - were bracing reminders of the trade ties being forged outside the United States as Washington moves towards a sharply more nationalist and protectionist agenda.
Merkel refused to give ground, even as she sought to ease the dispute with a rhetorical hug.
"Transatlantic relations are of paramount importance," Merkel said alongside Indian Prime Minister Narendra Modi in Berlin. "What I did was merely to point out that in light of the present situation, there are yet more reasons that we have to take our destiny in Europe into our own hands."
The Modi meeting was planned long before the dust-up with Trump. But the cheerful body language between the two leaders was difficult to miss.
"We are meant for each other," Modi said to Merkel, smiling widely, as both leaders made positive comments about a European Union-India trade deal in the works.
German officials - who say that the United States remains Germany's most important international ally and an important partner whose friendship they want to maintain - feel that Trump has prioritised relations with authoritarian nations such as Saudi Arabia instead of democratic allies.
Many were shocked when Trump declared in Riyadh that "we are not here to lecture" the mostly unelected assembled leaders - and then criticised European allies in Brussels for not spending enough on defence.
That led Merkel to conclude that she needs to advocate a sharply more pro-European agenda at home ahead of September elections, one ally said. She said on Monday at a beer-hall political rally that Europe can no longer fully rely on others, a message clearly about Washington, even if it was aimed largely at her own voters.
"It was mostly to say we have to strengthen Europe. It was not anti-Trump," said Norbert Röttgen, a close Merkel ally who is the chairman of the foreign affairs committee of the lower house of Germany's Parliament.
"You have to explain to your voters what we make of the experience of the last days," Röttgen said. "Trump, he is an unprecedented president. He calls into question by the way of his behaviour, by what he is saying, by what he is not saying, the foundation of this alliance, and you have to give an answer to that. And the answer of the Chancellor is that we have to bring into this alliance, not against this alliance, but into this alliance, a stronger German hand."
With Germany's elections drawing closer, Merkel has been forced to turn her attention to her own voters - most of whom loathe Trump and staunchly oppose increasing defence spending, one of his key demands. She is seeking a fourth term in office and has rejected most of Trump's criticisms as baseless.
Even before Trump's victory last year, Merkel was increasing defence spending, pushing up the budget by US$27 billion over the next three years. That would almost double current levels - but it would still be dwarfed by the US$664 billion the United States spends every year.
Now Merkel needs to convince German voters that defence increases are in their own interest, rather than a response to Trump. In a preview of election-season arguments, leading Social Democrats said that Merkel should have openly opposed Trump from the start rather than trying to work with him at first.
"Merkel needs to put some distance between herself and Trump, who is exceptionally unpopular in Germany," said Marcel Dirsus, a political scientist at the University of Kiel in northern Germany.
But there are practical limits to any German split from Washington, Dirsus said. Germany is not militarily independent and is far from becoming so. And the United States remains an important trade partner.
White House press secretary Sean Spicer said today that there was no dispute between Trump and Merkel.
"I think the relationship that the President has had with Merkel he would describe as fairly unbelievable," Spicer said.
But Europeans are growing weary of the message gap between Trump and the rest of his circle. They are still searching for which side to give greater weight - and last week's trip tipped the balance toward the President.
"Europeans think they are now being treated worse by Trump than countries like Russia or Saudi Arabia," said Stephan Bierling, an expert on transatlantic relations at the University of Regensburg in Germany.
The bilateral strains mean that the United States has, to some extent, lost the trust of one of Europe's most pro-American leaders. The German Chancellor, the most powerful politician in Europe, grew up in East Germany, and her upbringing there has long been credited for her staunch support for closer European-US ties.
"Given her experience with the Cold War, Merkel has long upheld and defended American ideals. But the belief in shared values has been shattered by the Trump Administration," Bierling said.
