The 1897 church closed earlier this year due to declining attendance numbers.
The windows - in memory of Tom McLean and Douglas Peterson, and the Rev Jim Steele - have been given to St Martin's Anglican Church in Duntroon and St Peter's Presbyterian Church at Tokarahi.
Rededication services were held recently at both churches.
Private Tom McLean served in the 21st infantry battalion during World War 2 and died on March 21, 1944, aged 27.
Prior to going to war, he lived at Island Cliff and was active in the Tokarahi Young Farmers Club.
Private Douglas Peterson died at sea on August 17, 1942, aged 27.
He was serving with the 26th infantry battalion.
He and Tom McLean's brother Jim were taken prisoner in North Africa and were being transported on a German ship when it was torpedoed by the British.
Pte Peterson did not survive and is buried in Greece.
One of the windows was jointly installed originally by the parents of Pte McLean and Pte Peterson, in memory of their sons.
The second window was installed with money raised by the congregation, in memory of Rev Steele who died in 1947 after 14 years' service to the parish.
He is buried at Duntroon.
In a book marking the Duntroon Presbyterian Parish's centenary in 1981, he was remembered as the "best kind of Scottish Presbyterian minister - friendly, conscientious, faithful, witty, learned and utterly committed to God".
