But now officials say what they hoped could be an early victory for the Trump administration by killing the ISIS leader has evaporated. New intelligence indicates the world's most-wanted terrorist leader no longer is hunkered down in Iraq's half-liberated, second-largest city -- and no one is certain where al-Baghdadi has gone or when he left.
"There was a sort of 'spidey sense' at that time that they were close, but that has gone away," one senior counterterrorism official briefed on the hunt told ABC News.
Al-Baghdadi's location was thought to be at a site with religious significance located within the city's crowded urban streets, which the U.S.-led coalition was reluctant to bomb because of possible civilian casualties and Muslim backlash if he wasn't there, another counterterrorism official said.
Being quicker on the trigger, however, became less relevant as it grew apparent in recent weeks that al-Baghdadi either wasn't cleverly hiding underneath a sacred religious site in Mosul or that he was there and somehow left it undetected.
"We don't think he's in Mosul anymore," a counterterrorism official involved in the campaign to destroy ISIS confirmed. "He's on the move."
For months, the U.S. military's most elite intelligence analysts had "assessed" with confidence that al-Baghdadi was not moving anywhere, dismissing speculative media reports early this year claiming the most wanted terrorist leader in the world moved around constantly, or that he was holed up in the de facto ISIS capital, Raqqa, Syria.
Had Obama or Trump flattened the Mosul sacred religious site where analysts began to suspect late last year that al-Baghdadi was hiding, it might have proven difficult to confirm his death with DNA -- even with the large network of human assets the military has cultivated there since the American war ended in 2011.
And bombing a site of religious significance also might have inflamed tensions throughout the Middle East.
Now some officials concede he might not have been in Mosul for months. No one knows for sure, as operators chase down hundreds of tips and American commandos from the Expeditionary Targeting Force attempt to capture senior ISIS operatives inside Syria.
"We have tons of intelligence reporting on al-Bagdhadi but nothing credible," the counterterrorism official told ABC News. "If he is still in Mosul, he's under a pile of rubble. But we're not sure where he is."
"He's probably hiding in a desert village somewhere," the official speculated.
Intelligence assessments are often mostly just that, speculation.
Though the U.S. Army's elite counterterrorism operators, Delta Force, were known to have operated covertly inside Raqqa for years, a ground force operation to capture Abu Bakr al-Baghdadi was never considered, an official said.
Unlike al-Qaeda leaders, al-Baghdadi is known to be surrounded by bodyguards believed to be strapped with suicide vests and heavy weapons, making capture effectively impossible.
"We've had a few leads on known associates that didn't pan out. But we'll get him. Just a matter of time," the second counterterrorism official said.
As Iraqi security forces guided by American military advisers move into western Mosul to eradicate it of an estimated 2,500 ISIS fighters, many wonder where another of the city's most recent residents is now -- the group's longtime British hostage, journalist John Cantlie.
Cantlie, forced to appear in many ISIS propaganda videos, was last seen in a video Dec. 13, 2016, looking more haggard as he showed the destruction of a bridge in Mosul.
Al-Baghdadi, his presumed chief captor, has only appeared on video once ever, delivering a fiery sermon in July 2014 from a Mosul mosque's pulpit and declaring himself "Caliph." His most recent message was a voice recording rallying his followers to defend Mosul last fall.
The U.S. military command headquartered in Baghdad did not immediately reply to a request for comment.