Van der Heyden says Armer has been on the board for six years and during that time has made a significant contribution to the progress of Fonterra.
"While we are disappointed that Colin has chosen to resign we respect his decision."
A replacement for Armer will be chosen at Fonterra's annual meeting later this year.
Armer was one of the three directors up for re-election this year. Others are chairman-elect John Wilson and Nicola Shadbolt.
Armer was one of the leading contenders for the Fonterra chairmanship. However, the board last week picked Wilson.