He has extracted from each commissioner a promise to resign if he should ask them to, and only a full-scale rebellion stopped him withdrawing their right to employ a press officer.
Nor is it just commissioners who are waking up to the Prodi style, with its grand visions and pledges redolent of his predecessor-but-one, Jacques Delors; one or two EU member states seem to be wondering if they have created a Frankenstein's monster. As one diplomat put it with understatement: "Where he is starting out is not where we would like to end up."
In London earlier this year Mr Prodi called for long-term plans for a European army. In a speech last week he set himself the task of forging a "new European soul", and foresaw an EU swiftly doubled in size to 30 states. Not only (to the alarm of the Finnish EU presidency) does he want to set firm dates for the accession of former Eastern European states, he also aims to deepen the EU. Last week he called for one "big bang" conference to change its rules to accommodate 15 new members, rather than just complete the tidying up left from the last treaty.
The contrast with the old regime could hardly be greater. After the high tide of Euro-integration led by Mr Delors, EU leaders chose an administrator of the lowest common denominator: Jacques Santer from tiny Luxembourg. When Mr Santer's commission imploded in March, prime ministers including Tony Blair saw Mr Prodi as a saviour able to regenerate the body.
Certainly the former prime minister of Italy is in a position of strength. The chaos left by Mr Santer's departure meant that his successor started with an unprecedented degree of support. Mr Prodi's powers within Brussels will be greater than those of his predecessors: apart from giving the President what amounts to an undated letter of resignation, the 19 commissioners will be banished from the Breydel building, the traditional HQ of the institution, to the offices occupied by the officials they control.
But is the commission president now going to find himself at odds with the EU's member states? A strong commission is guaranteed backing by the smaller countries, which see Brussels as a bulwark against the bigger powers. A fair proportion of the Prodi agenda is also welcomed by the big countries, including Britain: his emphasis on reform of the Brussels bureaucracy and economic modernisation will be welcomed in Downing Street.
On enlargement of the EU, his views are still within the mainstream. Joschka Fischer, Germany's foreign minister, is among those backing calls for a firm starting date for enlargement to be set at the Helsinki summit in December.
There remain flashpoints, however, including institutional changes where member states are committed to a minimalist agenda. By talking big, Mr Prodi is adopting the role of a poker player. "It is an opening bid," said an ally. "He knows that if you ask for a small IGC [InterGovernmental Conference], the commission will end up with almost nothing. It is important to hit first, and hit hard."
A rocky ride may lie ahead over the next five years.