He is expected to hail the reduction of forces as progress towards his 2016 election campaign promise to disentangle the US from "endless wars".
The presence of US troops has also become a major issue in Iraq since the US killed top Iranian general Qasem Soleimani in a drone strike in Baghdad in January.
What is the reason for the move?
During a visit to Baghdad, Gen McKenzie said the US military had confidence in the Iraqi Security Forces' increased ability to operate independently and to deal with the continuing threat of IS, which once controlled huge swathes of Iraq.
"In recognition of the great progress the Iraqi forces have made and in consultation and co-ordination with the government of Iraq and our coalition partners, the United States has decided to reduce our troop presence in Iraq from about 5,200 to 3,000 troops during the month of September," he told reporters.
"This reduced footprint allows us to continue advising and assisting our Iraqi partners in rooting out the final remnants of [IS] in Iraq and ensuring its enduring defeat," he added.
Gen McKenzie said the US would continue expanding "partner capacity programmes", and that its ultimate goal was having local forces who were capable of preventing a resurgence of IS and securing Iraq's sovereignty without help.
Why are US troops in Iraq?
In 2003, US-led forces invaded Iraq to overthrow President Saddam Hussein and eliminate weapons of mass destruction that turned out not to exist.
President George W Bush promised a "free and peaceful Iraq" but the country was engulfed by a sectarian insurgency that cost tens of thousands of lives.
US combat troops withdrew from Iraq in 2011 after President Barack Obama's administration failed to negotiate a new agreement governing their status.
In 2014, when IS seized control of large parts of Iraq, US forces returned at the invitation of the Iraqi government as part of an international coalition tasked with training and advising the Iraqi security forces.
The Baghdad government declared the military defeat of IS at the end of 2017 but about 5,000 US personnel remained to help Iraq prevent a jihadist resurgence.
Despite continuing attacks by IS sleeper cells, some Iraqi political groups - many of them linked to Iran - began demanding that US and other foreign troops leave.
Those calls attracted widespread support following the drone strike that killed Soleimani, an Iranian Revolutionary Guards commander who Mr Trump alleged was the "number-one terrorist anywhere in the world".