There are many reasons to believe that colder temperatures can affect your immune system. The chances are you’re not soaking in the sun as much as you do during the summer months, so you may be deficient in vitamin D. Vitamin D has been linked to a strong immune system, so this could be a reason for a weakened immune system during the winter months. Luckily, you can find vitamin D in several popular food items, such as pork products, mushrooms, fish, cheese, and eggs.