Eckhart Guth was Member of the Cabinet of the European Commission's Vice-President Haferkamp from 1979 to 1984. From 1985 to 1990, he worked in the Division Agriculture and Fisheries in the DG External Relations. From 1990 to 1993, he was Head of Unit Agriculture and Fisheries in the DG External Relations, and from 1993 to 1995, Head of Unit Relations with the United States of America in the same DG. From 1995 to 1999, he was Director of Expenditure in the DG Budgets. Eckhart Guth was Head of Cabinet of Commissioner Michaele Schreyer from 1999 to 2002, Deputy Secretary-General of the Secretariat-General from 2002 to 2006. From 2007 to 2009, he was Ambassador of the EU to the WTO and the international organisations in Geneva.

He was also Member of Commission delegation in international negotiations of GATT-Panels, OECD, International Sugar Organisation, Uruguay Round (1985-1995), Doha Round (2007-2009) - Chief Negotiator of the Final Agreement on Bananas with the US, the Latin American Countries and the ACP, as well as Participant as under-Sherpa of the European Commission President to the G8 Summits in Evian (France), Sea Island (US), Gleneagles (UK) and St Petersburg (Russia).