"I thought it was very important to come to the place where Islam began and to seek his majesty's counsel and discuss with him many of the issues that we confront here in the Middle East," Obama said before the talks began.
The meeting came as al-Qaeda leader Osama bin Laden accused Obama of "antagonising Muslims" in a tape broadcast by Al Jazeera.
On Tuesday, bin Laden's deputy, Ayman al-Zawahri, called Obama a criminal and warned Muslims to ignore his speech.
Two-state solution
Obama, whose father was Muslim and who lived in Indonesia as a boy, has made changes to many of George Bush's, his predecessor as president, policies that proved unpopular among Muslims.
He has ordered the closure of the Guantanamo Bay prison camp and set a date for the withdrawal of US combat troops from Iraq.
In an interview with the New York Times published on Wednesday, he said he hoped to persuade Arabs and their leaders to work with the US.
"There are a lot of Arab countries more concerned about Iran developing a nuclear weapon than the 'threat' from Israel, but won't admit it," Obama said.
There are a lot of Israelis, he said, "who recognise that their current path is unsustainable, and they need to make some tough choices on settlements to achieve a two-state solution - that is in their long-term interest - but not enough folks are willing to recognise that publicly."
King Abdullah had been expected to express his worries that Obama's diplomatic outreach to Iran may damage Riyadh's diplomatic strength, diplomats and analysts said, and urge Obama to increase pressure on Israel over the building of settlements.