Trump's first day of meetings with leaders of the military alliance was contentious, with Trump demanding nations spend far more on defense and accusing Germany of being "totally controlled" by Russian Federation because of a pipeline project.
Earlier Thursday, Trump called out US allies on Twitter as he attended a second day of meetings with leaders of the military alliance.
Trump said he had been "extremely unhappy" with allies' low levels of defense spending before the summit, but was pleased "they have substantially upped their commitment" during a "fantastic" unscheduled crisis meeting on Thursday morning. Says Stoltenberg: "We have agreed that we're committed to the pledge increasing defence spending to 2 percent".
In a separate briefing, German Chancellor Angela Merkel said there was a clear commitment to North Atlantic Treaty Organisation from all attendees.
"We will see what happens - just a loose meeting. My mother's family, for example, was divided by the building of the Wall", she said in remarks upon receiving the US Presidential Medal of Freedom in 2011.
The US leader has specifically singled out Germany for criticism over its defence spending.
Stoltenberg acknowledged that Trump had expressed himself in "very direct language" but insisted that away from the fiery rhetoric the allies all agree on fundamental issues: the need to boost NATO's resilience, fight terror and share the cost of defence more equally.
On day two, leaders will welcome non-NATO partners including Afghan President Ashraf Ghani and Ukraine's Petro Poroshenko to the alliance's new glass-and-steel headquarters as they seek to focus on policy rather than politics.
The President said: "We are supposed to be guarding against Russian Federation and Germany goes out and pays billions and billions of dollars a year to Russian Federation". Trump said he intends to talk to Putin about its alleged meddling in the 2016 USA election.
Mr Trump said countries needed to "step up, not over a 10-year period, they have to step up immediately" adding that other United States presidents had raised the issue but "did not do anything about it".
Germany, Europe's biggest economy, spends just 1.24 per cent, compared with 3.5 per cent for the US.
Alluding to Trump's comments about Germany, Kerry also said that "European energy security is an important topic for allies to discuss, even when they disagree".
"I don't think it should take a very long period of time and we will see where it leads but could lead to productive, something productive". We have a fundamental disagreements on principles and objectives between Trump and the Europeans.
Diplomats were already anxious about the summit ahead of time, not least because of an abrasive G7 meeting last month, when Mr Trump renounced a summit communique that had previously been jointly agreed.
Britain's Prime Minister Theresa May tried to ease the tensions on Wednesday by announcing additional troops for NATO's Afghan training mission, Reuters reported.
It was the most recent in a series of demands and insults that critics fear will undermine the decades-old alliance, coming days before Trump sits down with Putin at the conclusion of his closely watched European trip.