Microsoft will introduce measures addressing the EU's antitrust concerns about users' ability to choose different browsers.
EU antitrust regulators are investigating whether Microsoft blocks computer makers from installing rival Web browsers on its upcoming Windows 8 operating system, following complaints from several companies.
Almunia is in charge of antitrust enforcement at the European Commission.
"In my personal talks with Microsoft CEO Steve Ballmer he has given me assurances that they will comply immediately regardless of the conclusion of the anti trust probe," Almunia said at an economic conference in northern Italy, adding that he considered the matter a "very, very serious issue".
The affair is part of an investigation opened in July into the world number one software company's failure to offer users a choice of rival Web browsers which it had agreed with regulators three years ago.
In its latest spat with the US group, the EU watchdog is also looking into allegations that Microsoft does not provide access to complete interfaces (APIs) for non-default browsers in Windows 8.
Separately, Almunia said he was in favour of extending a temporary authorisation for state aid for stricken Franco-Berlgian bank Dexia beyond a 30 September deadline.
"But the most important thing is to advance on a final, structural solution about the future of the Dexia group," he said.