After the overthrow of the SMC by the AFRC led by Jerry Rawlings, Afrifa was again arrested on his farm at Mampong. Together with other arrested senior military officers, they were tried to varied extents in camera.
They were apparently found guilty of corruption, embezzlement, and using their positions to amass wealth. The investigations carried out were apparently incomplete. Evidence gathered by the National Reconciliation Commission in 2004 also suggests that the others executed were not properly tried. Previously, Afrifa had personally had his assets probed by the independent Sowah Assets Commission without any adverse findings. There also appears to have been a delay to the executions as no one including Rawlings appears to have been ready to sign the death warrants.
Afrifa had written a letter to Acheampong expressing fears about the future execution of soldiers as a deterrent against the staging of military coups in Ghana, due to the prevailing corruption and indiscipline in the military. This was around the period of the UNIGOV campaign and before Acheampong was removed in a palace coup on 5 July 1978.
“I feel greatly disturbed about the future after the government….
In order to discourage the military from staging coups in the future, how about if they line all of us up and shot us one by one? I do not certainly want to be arrested, given some sort of trial and shot. But I would be a stupid General if I sit in the comfort of my farm and await the VENGEANCE that is about to be unleashed on us…. I will pray to take away the fear and confusion weighing on my mind now.”
Lieutenant General Joshua Hamidu, a former Chief of the Defence Staff at the time of the AFRC regime, stated that he and Rawlings were the only soldiers at the center of government who opposed the executions of the former heads of state. He is quoted as saying in response to an accusation of calling for Afrifa’s execution that:
“That is ridiculous. It is a lie. I had nothing to do with the executions. For three weeks after the 4 June event, questions were constantly raised about executing people. I always stood against it. Surprisingly, the only person who also stood against it was Rawlings. The young boys wanted blood and I used to tell ‘you cannot resurrect the man once you’ve killed him. If you have any case against people, try them. Let everybody hear what they have done wrong against the country.’ And that even, they could not do.”
Acheampong was in the garden when he was arrested together with two other former Heads of State (Gen. Afrifa and Gen. Akuffo) and five other senior military officers (Amedume, Boakye, Felli,Kotei and Utuka).
On 26 June 1979, Afrifa was executed by firing squad, together with General Fred Akuffo and others. Reports suggest that Afrifa did not die immediately and had to be shot again. The bodies of the executed officers were buried without ceremony at the Nsawam Prisons Cemetery at Adoagyiri, near Nsawam in the Eastern Region.