On the last leg of his final European tour as president, Obama will underline shared values, try to ease fears about the future of the transatlantic partnership and thank Merkel for her friendship during his two terms, White House officials said.
As Western leaders brace for potentially radical changes with Trump moving into the Oval Office in January, Obama wrapped up a visit to Athens Wednesday warning that globalisation required a "course correction" to keep voters from drifting to extremes.
"When we see people, global elites, wealthy corporations seemingly living by a different set of rules, avoiding taxes, manipulating loopholes... this feeds a profound sense of injustice," he said.
After Trump's shock victory, Merkel expressed a desire to maintain close ties with Washington.
But in an extraordinary break with tradition for Germany, which long saw the US as its protector and closest partner, Merkel pointedly said cooperation must be based on shared democratic principles and respect for human dignity.
Analysts said the meeting Thursday could be seen as a kind of passing of the torch from Obama to Merkel, whom he's called "probably... my closest international partner", for stewardship of the free world.
Obama held the biggest rally of his 2008 campaign in Berlin, using the once-divided city's rebirth as a symbol of progress as he made a hopeful call for a world without nuclear weapons to 200,000 cheering fans at the Victory Column monument at sunset.
He and Merkel, who took power in 2005, soon developed a strong partnership, despite rifts over revelations of NSA spying on Merkel's mobile phone and Obama's vocal opposition to Germany's austerity-driven response to the European debt crisis.
Germans at the Victory Column on a grey November day hours before Obama's arrival said they were sad to see him go and anxious about what the Trump administration would bring.
"We were so hopeful after George W. Bush left office," said Thomas Schmidt, 54, a business clerk who recalled being "thrilled" when he watched Obama's Berlin speech on television.
"It was a euphoric mood, a little bit like when the Berlin Wall fell. The feeling now with Trump is much more wary. No one knows what he might do."
Hannah Müller, a 26-year-old linguistics student, said Obama had failed to live up to many Germans' expectations in his inability to close the military detention centre at Guantanamo Bay or advance peace in the Middle East.
"Trump made a terrible impression here during the election campaign but at least he won't disappoint us," she said.
Matthias Krah, 43, an IT project manager, found the prospect of Trump in the White House "scary" and predicted a major realignment of transatlantic ties.
"It means we Europeans will need to look inward. Maybe we can start doing without the US," he said.
Opinion polls show the vast majority of Germans did not support Trump's race for the White House.
Two out of three now say they fear ties with Washington will suffer under the new administration, according to a survey last week for public broadcaster ZDF.
Only three percent thought relations would improve, while 60 percent said that the number of international conflicts was likely to rise under President Trump.
Obama dined with Merkel at his hotel late Wednesday and will hold talks with her at her chancellery Thursday followed by a meeting Friday including the leaders of Britain, France, Italy and Spain.
While in Athens, Obama issued a stern warning against "crude" nationalism,
calling the NATO alliance "absolutely vital" to US interests and stressing a strong, unified Europe was good for America.
The comments were directed at nations jittery over Trump's critical comments about transatlantic relations.
Obama has relied on Merkel's strength in Europe on several fronts including helping to defuse the Ukraine conflict, taking in hundreds of thousands of Syrian refugees and promoting free trade.
As he exits the stage, many observers say Merkel's importance as a defender of Western values will only continue to grow, assuming she - as expected - runs for a fourth term next year.
"A lot about Europe's future will be determined by whether Germany has a strong leader who wishes to push things forward," said Daniela Schwarzer, director of the German Council on Foreign Relations.