Windass, played by Mikey North, went AWOL earlier this year after meeting a soldier who was injured at war, but will overcome his fears by disarming improvised explosive devices.
The new storyline comes after show bosses decided to move away from typical domestic dramas, according to the News of the World.
A source said: "We will not be holding back on the realities of our men and women going to war. We'll be showing how it really is, warts and all."
Writers at the ITV1 soap are said to have consulted the Ministry of Defence regarding the storyline, which will be shown on-screen in October.