The Finnish Institute at Athens is classified, according to Greek legislation, as an archaeological school, and is therefore allowed to carry out archaeological fieldwork in Greece. Such projects are mainly funded by different Finnish foundations and universities.

The Institute’s first excavation concerned the Early Christian basilica at Arethousa in northern Greece. The actual fieldwork of the project, directed by Arja Karivieri, took place between 1999 and 2002. In 2000 and 2001 a second project, directed by Jari Pakkanen, was organised in Stratos, western Greece. It aimed to create a 3D model of the Temple of Zeus at Stratos through an exact measurement of the temple's architectural remains.

A third project, directed by Erkki Sironen, began in 2003. It aims to re-study all known Roman epigrams in Greece. Finally, a multidisciplinary project studying the history of the Kokytos river basin in Thesprotia, north-western Greece, began in 2004 under the directorship of Björn Forsén.

Before the Institute had archaeological projects of its own, Finnish scholars acquired experience by participating in, among others, Greek, Norwegian and Swedish excavations and surveys. A good example of Nordic collaboration is the excavation of the temple of Agios Elias at Asea in the Peloponnese. This project, which was directed by Jeannette Forsén under the auspices of the Swedish Institute at Athens, brought together researchers from Norway, Sweden and Finland.