The time had come to stop the rot. A whispering campaign in the international press had even suggested Mr Romano Prodi wanted to throw in the towel and return to Italy. And among the Commission staff the pledge of root-and-branch reforms had spread resentment and fear. Morale was at rock bottom.
But yesterday the Commission president hit back. His much-criticised spokesman, Mr Ricardo Levi, would move on and the Commission machine would get a new dynamic from a young boss with a reputation for straight dealing and toughness, Mr David O'Sullivan.
Mr Prodi is most definitely here to stay, and the message is, at last, loud and clear: "Full steam ahead!"
From an Irish perspective it was good news, too, propelling one of our own to the most senior position held by an Irish figure in the EU institutions. But, as Mr O'Sullivan is careful to insist, he is not here in a representative capacity but as an impartial European civil servant who can, however, contribute a sensitivity to Irish perspectives on key issues.
That small-state perspective will be welcomed in other capitals, too, at a time when many of them feel the need to reassert their role and that of the Commission as defender of the treaty and "friend of the small states".
Mr O'Sullivan is deeply committed to continuing European integration to the point occasionally of exasperation at what he sees as Irish foot-dragging and lack of nerve on constitutional issues.
But his key challenge is undoubtedly the management of reform in a Commission deeply demoralised by outside criticism and concerns at what many see as the pursuit of change for its own sake. Convincing staff that change is not only inevitable but in their interests would be difficult, "painful, traumatic and destabilising", he admits. "But the option of not changing is simply not an option."
That process involves not only improving efficiency but also redefining more clearly the role the Commission should be playing. Over the years, he admits, the EU's executive arm has taken on more than it can handle, and part of the Prodi agenda to which Mr O'Sullivan is strongly committed is the idea of re-nationalising elements of the administration in a framework that allows Brussels supervision but not day-to-day operational control. The Commission can then return to its primary role of policy initiation.
Crucial to that process will be his relationship with the Vice-President responsible for Administrative Reform, Mr Neil Kinnock, and the latter's new chef de cabinet, Mr Philip Lowe, whom Mr O'Sullivan knows well.
But he should have a freer hand than his predecessor, Mr Carlo Trojan, as Commission sources suggest there will be a significant strengthening of the secretary-general's role at the expense of the President's cabinet, particularly in the detailed follow-up of policy.
Mr O'Sullivan's promotion by Mr Prodi is undoubtedly a vote of confidence in somebody who has had considerable management experience within the institutions and has made surprisingly few enemies.
Mr Prodi's relations with the press should improve, too, with the departure of the congenial but ineffective Mr Levi to take charge of a revamped think-tank, the Forward Studies Unit, now the Economic and Political Council. He will remain in daily contact with Mr Prodi, advising on practical policy actions.
Mr Prodi yesterday refused to blame Mr Levi, his friend and confidant, for the Commission's communications failures but acknowledged pragmatically that if relations between his spokesman and the press were poor, whoever was responsible, the situation had to be remedied.
Mr O'Sullivan is replaced as chef de cabinet by a French man, Mr Michel Petite, also from the cabinet, who served under Mr Jacques Delors. Mr Petite, who knows Ireland well having visited the country many times, is a lawyer who has particular expertise in institutional issues and was one of the key figures in the drafting of the Amsterdam Treaty.