The Commission wants Microsoft to provide rivals with enough information to develop software that could run as smoothly as its own on Microsoft's Windows operating system.
Changing tack?
Microsoft's lawyer Ian Forrester claimed on Wednesday that the ruling would handicap the market leader "in perpetuity".
"The Windows source code is copyright. It is valuable, the fruit of lots of effort," he said.
Thomas Vinje, one of the lawyers arguing against Microsoft, said that the software company was trying to change the parameters of the dispute.
"Microsoft are trying to turn this into an intellectual property case when it's not," he said.
"This is a case about abuse of a dominant position, about refusing to provide information to vendors."
Microsoft's challenge at the EU's Court of First Instance could have widespread ramifications for future competition rulings by the Commission if the court's 13-member panel rule in its favour.
Microsoft's appeal is being heard over five days, although a decision in the case is not expected for months, or possibly a year.
It could be further appealed to the European Court of Justice on a point of law.
In the meantime, Microsoft is facing fines of up to 2m euros a day if it is found to have delayed its compliance with the anti-competition ruling.