Microsoft and the Commission reached agreement in October that Windows users will be presented with a ballot screen in which they can change from Internet Explorer to one of 11 other browsers if they choose.
"This was the last cloud in our relationship, and I think that cloud is gone," said Jan Muehlfeit, the chairman of Microsoft in Europe, at the Cebit trade show. "We are very glad we put it behind us."
The agreement came after a decade-long battle, with Microsoft accused of antitrust violations in how it promoted Internet Explorer. The company was also accused of not making enough interoperability information available to competitors so they could make their products compatible with Windows.
On Tuesday, the European Commission issued a statement praising the launch of the browser choice programme, saying that the ballot screen is expected to be displayed on 100 million computers in Europe by mid-May.
"More competition between web browsers should also boost the use of open web standards, which is critical for the further development of an open internet," according to a statement attributed to Joaquin Almunia , the European Union's competition commissioner.
Users who buy a new PC will also be presented with the ballot screen. Microsoft is committed to the ballot programme for five years, and the company will submit regular reports to the Commission.
Computer manufacturers can now install other Web browsers on Windows computers alongside Internet Explorer. As part of the agreement, Microsoft said it would not retaliate against manufacturers that install other browsers on new PCs, the Commission said.
Muehlfeit said the agreement with the Commission also marks how Microsoft has changed over the last decade, with the company coming up with the technical solution after hearing the Commission's concerns.
"It was a different industry 10 years ago when the antitrust issues started," Muehlfeit said. "Do I think we went through a learning process? Yes."