Omonoia has four affiliates in the cities of Sarandë, Delvinë, Gjirokastër and Tirana, and some sub-sections in Korçë, Vlorë and Përmet.

It called for the autonomy of Northern Epirus in 1991 on the basis that the rights provided for the minority under the Albanian constitution were highly precarious.

[5] Omonoia was banned from contesting the 1992 elections on the grounds that it violated an Albanian law forbidding the 'formation of parties on a religious, ethnic and regional basis'.

Four of the five ethnic Greek members of Omonoia stated that, during their detention, authorities subjected them to physical and psychological pressure, including beatings, sleep deprivation, and threats of torture.

[10] In early October 2011, the Albanian government announced that a census would be conducted throughout the country, which would count the exact size of ethnic minorities for the first time after 1989.

During the time the census was conducted, half of this number resided permanently in Greece, but maintained strong contacts with its homeland.

[16] In January 2012 the leader of the Korçë branch of Omonoia, Naum Disho (Greek: Ναούμ Δίσιος Naoum Disios), was sentenced to prison for constructing a memorial for the fallen Greek soldiers of the Greco-Italian War in Boboshticë, due to accusations of desecrating ethnic Albanian graves,[17][18] however his sentence was overturned.