In a large bowl, combine the milk, yogurt, eggs, vanilla, and brown sugar. Whisk the wet ingredients until smooth.
In a separate smaller bowl, mix together the flour, baking powder, salt, and cinnamon. Prepare the apples by coring chopping in fine pieces, to get 2 cups of apples.
Preheat the waffle iron so that it is ready by the time you finish making the batter.
Place the dry ingredients in the wet ingredients. Use a whisk to gently combine the two together. The batter should stay lumpy, and not overmixed. Add the apples pieces and use a rubber spatula or large spoon to fold them in the batter, again, without overmixing the dough.
Once the waffle iron is at temperature, spray the inside with non-stick spray. Follow your waffle iron's consideration for the amount of batter it suggests. When making them in a single 8-inch waffle, it takes 1 ¼ cup of batter.
Once the waffle is lightly golden, remove it from the iron and repeat the previous step until the batter has been used up. Serve right away.