Obama, who described Merkel ahead of the visit as his "closest international partner", will dine with the chancellor at Berlin`s famous Adlon hotel directly next to the landmark Brandenburg Gate on Wednesday evening.
The two leaders, who together tackled the global financial crisis, promoted free trade and forged an international accord to fight climate change, stressed their shared values in a joint guest piece for German magazine Wirtschaftswoche.
"There will be no return to a world before globalisation," they wrote, stressing the benefits of a free trade deal being negotiated between the European Union and the United States.
Trump, a billionaire businessman with no previous experience of public office, made attacks on international trade deals a cornerstone of his election campaign, saying they have cost U.S. jobs.
His election win heralds a hard break in a relationship that grew extremely close during and immediately after the Cold War.
It wobbled when Berlin refused to go along with U.S. President George W. Bush`s Iraq war in 2003 and Germany and France were derided by his Defense Secretary Donald Rumsfeld as "old Europe".
But the relationship has again flourished in recent years, with Obama and Merkel also leading an international push for economic sanctions on Russia over its role in the Ukraine crisis. Trump by contrast has spoken warmly of Putin.
Last week Merkel, Europe`s most powerful leader, offered to work with Trump on the basis of their countries` shared democratic values.
Merkel and Obama will hold bilateral talks on Thursday before they are joined on Friday by the leaders of France, Britain, Spain and Italy.
It is Obama`s last trip to Europe as president before he hands over to Trump in January.