In a tweet, the US president said America had a "massive trade deficit with Germany" and warned: "This will change," the Independent reported.
It came after the German Chancellor said her country can no longer rely on the US under Trump's presidency.
Speaking at a campaign event held in a Bavaria, Merkel emphasized the need for friendly relations with the US, Britain and Russia, but added: “We Europeans must really take our destiny into our own hands.”
Merkel said that as the traditional Western alliance is threatened by the new US presidency and Brexit, “the times in which we can fully count on others are somewhat over".
Her comments came after Trump said he needed more time to decide if the US would continue backing the Paris climate deal, which has frustrated European diplomats.
On Monday, Merkel again underlined her doubts about the reliability of the US as an ally but said she was a "convinced trans-Atlanticist", fine-tuning her message after surprising Washington with her frankness a day earlier.
"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," Reuters quoted Trump as tweeting on Tuesday.
The image of friendly relations between Germany and the US seems distant since Trump took office. His administration has previously said that Germany's trade surplus is a result of the country's manipulation of the euro.
Germany fought back arguing that it doesn't have powers to manipulate the euro and the only reason consumers opt for its products is because they are more competitive.
Meanwhile, contributions to the defense alliance NATO has emerged as another problem between Berlin and Washington. Trump has repeatedly asked NATO allies to step up their contributions. At the moment, only 5 of the 28 members fulfill the target of paying at least 2 percent of their gross domestic product (GDP) on defense, cnbc.com reported.
According to NATO data, Germany is currently spending 1.2 percent of its GDP on NATO. The US spends 3.6 percent.
Germany, like other NATO members, vowed to present an action plan on how it's planning to increase defense spending at a summit last week. At the time, Trump told his allies they were being unfair towards US taxpayers.