In March 2006, Barnier was elected vice president of the European People's Party (EPP) for a three-year term. Under Nicolas Sarkozy's presidency, upon the reshuffle of the French cabinet, caused by the resignation of Alain Juppé after the 2007 French legislative election, he re-joined the French Cabinet as Minister of Agriculture.

Barnier worked in 2006 as a special adviser to José Manuel Barroso, the then President of the European Commission, and presented a report to the Council of Ministers proposing the creation of a European civil-protection force. In 2006–2007, he served as member of the Amato Group, a group of high-level European politicians unofficially working on rewriting the Treaty establishing a Constitution for Europe into what became known as the Treaty of Lisbon following its rejection by French and Dutch voters.

From 2015, Barnier served as unpaid Special Adviser on European Defence Policy to President of the European Commission Jean-Claude Juncker.