The US will take control of about 8,000 British troops in Helmand province, southern Afghanistan, later.
The move is part of a restructuring of Nato forces, with command and control in southern Afghanistan split into two.
Defence Secretary Dr Liam Fox welcomed changes he said were "based on sound military rationale" and in the interests of the coalition strategy.
The UK force level in Afghanistan is currently 9,500, and including special forces, totals some 10,000.
Until now, UK forces took their orders from British Major General Nick Carter, who was in charge of operations in the south.
But the region is being split to make it more manageable.
Gen Carter will oversee Kandahar and Maj Gen Richard Mills, of the US Marine Corps, will command forces in Helmand.
Maj Gen Gordon Messenger told BBC Radio 4's Today programme: "To the guys on the ground it will make very little difference at all.
"It's absolutely normal business when you are working on a Nato operation that officers of different nations will command you at one time or another."
The defence secretary said British forces had made "real progress in Helmand", adding that they would "continue to do so working alongside Afghan, American and other Isaf partners making up an international effort of more than 45 nations".
Maj Gen Messenger said that providing security was the "bedrock" on which a peaceful Afghanistan would be built, but that had to be followed up by good governance in the country.
"Ultimately the key to this is the allegiance of the population," he added.
"When the population demonstrate their allegiance to the Afghan government, we will have done our job."