The windows celebrate the legacy of former minister Patrick Bell, who also revolutionised farming by inventing the reaper machine.
They will be unveiled over the next week.
The renovation work focused on a rose and double lancet combination, which was originally designed by famous stained glass artist Adam Stephen in the early 20th century.
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It has biblical references around it, as well as images of the reaper, an invention Patrick Bell refused to patent as he wanted it to stay accessible to all.
The rural Church of Scotland building was constructed in 1609, with additions made in the nineteenth century.
Current minister of the church Stewart Lamont said: ''The people of Carmyllie Church are very strong in conserving their heritage.''
Carmyllie Church will be open to the public this weekend from 10am to 4pm on Saturday and 11am to 4pm on Sunday.
All are welcome to attend the church's Sunday service at 9.30am.
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