After training in business and finance law, Moutarlier began his career as a tax lawyer at Francis Lefebvre Bureau, a prominent French law firm, before joining the European Commission in 1993.
Over the following decades he held a broad range of roles, starting in DG Taxation and Customs Union and DG Budget, before moving to DG Enterprise and Industry in 2003, where he led the Strategic Planning Unit and subsequently oversaw the establishment of Copernicus, the EU's European Earth Observation Space Programme. He then served as Cabinet Expert to Commissioner Šemeta (tax policy, 2010–2014), followed by a senior directorial role in DG TAXUD covering direct taxation and economic analysis.
In December 2019, he became Head of Cabinet to Internal Market Commissioner Thierry Breton, gaining deep exposure to EU industry, digital, defence and single market policy. After a period as Senior Adviser at DG TAXUD, he was appointed Deputy Director-General for European Industry and Decarbonisation at DG GROW in October 2025, bringing over 35 years of professional experience — more than 30 of them at the European Commission.