Initial investigation by the Commission found that the proposed transaction might significantly impede effective competition, particularly in the German magazine market, where the joint venture would have a combined market share of over 40%.
However since the transaction also covers catalogues and advertisements, part of a larger cross-border market, the Commission decided not to refer the case to the German competition authorities.
A statement issued by the three firms said they welcomed the decision of the Commission to handle the case in Brussels "given the pan-European nature of the high volume printing market in which the companies operate".
The transaction, which was notified to the EU on 4 November, includes Arvato's 115m planned gravure factory in Liverpool.
The Commission has 90 working days to reach a conclusion.