The church has undergone major earthquake strengthening and the windows cap off that project.
The second and final stage in the upgrade will include a covered courtyard and entry between the church and existing hall, a parish office and a minister's office.
Church spokesman David Bennett said it was decided that in any window the cross was to be a central element.
"The smaller crosses below symbolise the sacrifices others made in time of conflict," he said. "While many who served in war gave something, there were many who gave everything. The red poppies recall the sacrifice of so many, while the nine small crosses memorialise those from our parish who died in service."
Mr Bennett said the glass depicting the grassy hillsides captured the movement of windblown grass on a Westmere hillside which was a reference to the local identity of the men who served.
"The tree in the centre is a pohutukawa and is in the context of the burning bush - this is the symbol of the Presbyterian Church and reflects the bush that did not burn and attracted Moses to the voice of God in the Old Testament.
"There are also red poppies and various country scenes of grass, sky, sea and clouds."