At Oxford, she also chairs the RENEW programme (Rethinking Europe in a Non European World), the Euro-Mediterranean network RAMSES, coordinated by the Maison Méditerranéenne des Sciences de l'Homme in Aix en Provence, and the EU-WTO Oxford programme in collaboration with the German Marshall Fund.

From 1996 to 2004, she advised prominent Greek politician, George Papandreou on European affairs during his first term as Foreign Minister of Greece.

She was advisor to the 2004 Dutch Presidency of the Council of EU on the theme of "Europe: a Beautiful Idea", a policy-academia dialogue culminating in the December 2004 intellectual summit.

Much of Nicolaïdis' recent work focuses on "European demoi-cracy" and the challenge of building an EU of deep diversity through the mutual recognition of identities, polities, and socio-economic rules.

She has published widely on EU institutional and constitutional debates, EU external relations including with Mediterranean countries and the United States, issues of identity, justice and cooperation in the international system, the sources of legitimacy in European and global governance, the relationship between trade and regulation, trade in services as well as preventive diplomacy and dispute resolution.