The US leader was led in by European Council President Donald Tusk ahead of a summit of NATO leaders at the military alliance's headquarters in the city later in the day.
Following an initial round of talks with President Trump Donald Tusk said they seem to have "differing positions" on dealing Putin, climate change and global trade.
Tusk said in a televised statement the two leaders agreed on countering militant violence and on relations with Ukraine.
He said: "We discussed foreign policy, security, climate and trade relations," Tusk said in Brussels after he and EU chief executive Jean-Claude Juncker met Trump for an hour.
"My feeling is that we agreed on many areas, first and foremost on counter-terrorism."
Trump, on the fourth leg of his first foreign trip since taking office also met European Commission President Jean-Claude Juncker.
The trio posed for cameras before making small talk about Trump's trip.
Mr Juncker said he "had been following" Trump's travels around the Middle East with Mr Tusk saying the greeting in Saudi Arabia was "spectacular".
President Donald Trump walks beside Belgium's Prime Minister Charles Michel at Brussels airport
Donald Trump and Donald Tusk sat down opposite each other
Meanwhile friends Angela Merkel, the German chancellor and former US president Obama appeared together at a talk called 'Being Involved in Democracy: Taking on Responsibility Locally and Globally' at Brandenburg Gate.
The President of the United States has been cryptic over his true feelings on the EU, bouncing between calling it a "vehicle for Germany" and a "wonderful institution".
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Mr Trump, who once labelled Brussels a "hellhole", have touched down in the city following his Middle Eastern tour for a first-hand look, and a NATO summit.
Thousands took to the streets of the city to protest the arrival of the Trumps.
In January 2016 he attacked their home, calling it a "hellhole" because of Muslim immigration.
Donald Trump (C) and US defence minister, James Mattis meets with Donald Tusk
Donald Tusk met Donald Trump before leading him to meet heads of European Union institutions
He will be there for just 36 hours – but the events will make a big difference to relations going forward.
Pro-European chiefs have long been at odds with the nationalistic Trump regime, as they advocate single rules for multiple nations, and Mr Trump wants the US to come first.
The EU will want to hammer out difference with the US from trade to climate change.
Meanwhile, protesters were arrested outside the meeting.
Donald Trump and Tusk gesture at each other before meeting
Donald Trump (R) shakes hands with EU foreign policy chief Federica Mogherini
Donald Tusk and Donald Trump looked tense entering the meeting
A senior EU official said: “We all remember the mood which we had here not only in Brussels but all around Europe — that is anxieties and sometimes even fears on the direction which the new American administration will take, especially or in particular vis-a-vis the integration of the European Continent.”
Mr Trump himself appeared to be pro-Brexit and anti EU in the run-up to his election.
He openly spoke about countries quitting the bloc.
Streets were closed off for the arrival of Mr Trump and the First Lady who headed first to the Belgian royal palace to meet King Philippe and Queen Mathilde.
Mr Trump then met Prime Minister Charles Michel.
Donald Trump in Brussels
Thu, May 25, 2017
Donald Trump has arrived in Brussels for talks with European leaders at the European Council
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Donald Trump talks with President of the European Council, Donald Tusk
Angela Merkel met with former President Obama on Thursday
Donald Trump and Melania arrive in Brussels for round of meetings
We have tried to avoid moving him around in an untimely way in Brussels
Michel’s spokesman, told POLITICO: “We have tried to avoid moving him around in an untimely way in Brussels."
Despite Mr Trump's comments on the capital in the past, Cauderlier said Trump's “first words were about his joy and pleasure to be in Brussels”.
Mr Trump and wife Melania are reportedly staying just a five-minute walk from the palace, across the Parc de Bruxelles.
There are three empty residences belonging to the US in Brussels since there is no United States ambassador to Belgium, to the European Union, or to NATO.
Donald Trump is due to meet European Council President Donald Tusk and European Commission President Jean-Claude Juncker this morning.
More campaigners are expected to take to the streets to vent their anger at the visit.
A meeting with French President Emmanuel Macron will follow before the president heads to NATO – an organisation he called "obsolete" – until his meeting with Jens Stoltenberg.
Donald Trump (2ndL) and first lady Melania Trump (R) pose with King Philippe and Queen Mathilde
An EU official told Politico: “I think now being in a situation where we can not address existential questions but talk about business, talk about cooperation, is in itself a measure of progress which took place in these last few months.”
Mr Trump said following the attack in Manchester where 22 Ariana Grande fans, as young as eight, were slaughtered by a suicide bomber.
The US president, who is travelling with the secretary of state, Rex Tillerson, added: “We have different problems to discuss, but number one is terrorism. We are in a terrible situation, but we will win.”