PEER participation in FP6 is strongest in five projects: ALARM, Euro-limpacs, NoMiracle and Sensor. These projects involve at least four of the PEER member organisations, and they are jointly called "Flagship projects".

Other projects with strong participation from several PEER centres include EBONE, NeWater, NitroEurope, PLUREL and SCENES.

METIER (METhods of Interdisciplinary Environmental Research) is a Marie Curie Series of Events offered by PEER members and funded by the European Community.