Despite Armagh's disappointing 2016 season, McGeeney and his assistant Aidan O'Rourke have been given a vote of confidence by the Armagh GAA board.
McGeeney has relinquished his managerial role with the county's Under-21s which now be taken by former county senior boss Peter McDonnell.
Ex-county stars Martin McQuillan and Diarmuid Marsden will assist under-21 boss McDonnell.
After losing the Kildare senior job in 2013, McGeeney served as Paul Grimley's Armagh assistant in 2014 before moving up to the Orchard County's main managerial role for 2015.
McGeeney guided Armagh to the Division Three Football League title in 2015 before they endured a disappointing championship campaign as a comprehensive Ulster Championship defeat by Donegal was followed by an early qualifiers exit against Galway.
Armagh then endured a disappointing 2016 as they suffered relegation back to Division Three before an opening 2-16 to 0-14 Ulster SFC defeat by Cavan was followed by two losses against Laois in round one of the qualifiers.
Laois' initial 1-10 to 0-10 win over Armagh had to be replayed after the Leinster county was found to have played one substitute too many but Laois also won the replay 1-11 to 1-10.
Following Armagh's Ulster Championship defeat by Laois, RTE GAA pundit Joe Brolly strongly criticised McGeeney's managerial abilities and this led the Armagh county board releasing a statement defending the manager.
Kieran McGeeney will be remaining on as Armagh football manager in 2017.