The EU's second highest court disagreed with these allegations, however, ruling in July that there was not enough evidence to demonstrate that the tech giant broke EU competition rules.
"The General Court annuls the contested decision because the Commission did not succeed in showing to the requisite legal standard that there was an advantage for the purposes of Article 107(1) TFEU," the judgment [PDF] said.
In announcing the appeal, the commission said it believed the General Court had made a "number of errors of law" when making its judgment.
"We have to continue to use all tools at our disposal to ensure companies pay their fair share of tax. Otherwise, the public purse and citizens are deprived of funds for much needed investments -- the need for which is even more acute now to support Europe's economic recovery," European Commission EVP Margrethe Vestager said in a statement.
"If Member States give certain multinational companies tax advantages not available to their rivals, this harms fair competition in the European Union in breach of State aid rules," Vestager added.
The EC originally made these allegations against Apple back in 2016, after a two-year investigation had found that Ireland issued two tax rulings to "substantially and artificially" lower Apple's tax bills.
The deal allegedly saw Apple attribute all profits from two of its incorporated companies to a "head office" in Ireland, which had no employees and "could not have generated such profits", the EC said at the time.