Few lined the motorcade route to the city after Trump arrived at a military airfield for his much awaited visit to Brussels.
Soon after his arrival in Brussels, a city he once attacked as a 'hellhole', he met Belgian Prime Minister Charles Michel and told him that the world was "in a terrible position" but that terrorism would be defeated.
Belgian police said they believed that about 6000 people had joined protests on Wednesday evening, although further demonstrations were expected through the night.
On Thursday Trump will first meet European Council President Donald Tusk and his European Commission counterpart Jean-Claude Juncker, having previously supported Britain's shock Brexit vote and claiming the EU was a doomed would-be superstate.
He will then hold his first summit with the 28 leaders of the Nato military alliance, which he dubbed "obsolete" on the campaign trail, where he is expected to press them to join the US-led coalition against Islamic State.
An EU source said that increasing defence spending and doing more to fight terrorism will be high on the agenda, while the EU is expected to raise the importance of keeping trade open and climate action.
The visit has been slightly overshadowed by the terrorist attacks in Manchester, with British Prime Minister Theresa May said to be furious at US intelligence officials over leaking of operational intelligence from the police investigation into the suicide bomb attack on Monday
The name of the attacker and photographs reported to be images of the crime scene taken by British investigators were published Wednesday.
However, at a press conference on Wednesday, Nato Secretary General Jens Stoltenberg set a more conciliatory tone, hailing Trump's plan to expand, with $4.8bn, the European Reassurance Initiative, a military fund to counter Russian aggression.
Shortly before Thursday's summit, Belgium will formally hand a new 250,000 square metre building over to Nato in the presence of the Belgian king - the site is Belgium's first ever airfield, dating back to 1908, and was occupied during both world wars.
Turkish President Recep Tayyip Erdoğan will also attend the Nato summit but, unlike his last visit to the city, this is expected to be free from protests, after the Brussels mayor and police banned them.
Senior EU figures are hoping that this week's visit and his face-to-face meetings with EU leaders could be a good opportunity to take the first steps to heal a rift in relations between the two sides.
Relations between the two sides soured in April when the European Parliament adopted a resolution that said US visitors to the EU should be forced to buy visas because of America's travel restrictions on a handful of EU member states.
Several European leaders also rejected Trump's anti-Muslim and much-criticised travel ban amid concern over his commitment to transatlantic values.
The ban, on refugees and citizens of seven Muslim-majority countries, saw European capitals scramble to determine how it would affect their dual nationality citizens.
Despite some pessimism there are hopes that Trump's visit to Brussels may pave the way for improved EU-US relations in the coming weeks and months.
Lately, Trump has appeared to soften his stance on the EU.
In a meeting on 20 April with Italian Prime Minister Paolo Gentiloni, he said that a strong Europe was "very important" to him and the United States. His assurances break with earlier statements during Trump's election campaign when he praised Brexit and called the EU a "vehicle for Germany". Trump also called for "balanced, reciprocal" trade relations with Italy.