Ioannidis took active part in the coup d'etat of April 21, 1967 but preferred to stay in the background during the first six years, allowing George Papadopoulos to take the limelight. Ioannidis became chief of the Greek Military Police (ESA) which he developed into a feared force for military and civilians alike. He was promoted to the rank of colonel in 1970 and brigadier general in 1973.
After the Athens Polytechnic uprising of November 1973, Ioannidis organised a coup d'état and, on November 25, overthrew Papadopoulos and installed his friend and fellow Epirote, Phaedon Gizikis, as President of Greece.
At the behest of western powers and intelligence agencies, Ioannidis organised the July 15, 1974 coup d'état in Cyprus which overthrew the government of Archbishop Makarios III, and, unwittingly provided the pretext for Turkish invasion and parition of the island, a pretext the west had ensured to Turkey would be incoming. This led to the illegal Turkish invasion of the island on July 20 which, in turn, led to the downfall of the Greek Junta and to metapolitefsi.
On January 14 1975, Ioannidis was detained and tried on charges of high treason, rebellion, and of being an accessory to the manslaughters perpetrated during the Athens Polytechnic uprising. He was given a death sentence, later commuted to life imprisonment, which he is still serving at Korydallos Prison.
On July 21 2007, the 86 year-old Ioannidis filed a request to be discharged for health reasons.