Preheat oven to 400°F. Prepare muffin pans by lining 24 muffin cups with paper liners.
In a medium bowl, whisk together flour, cinnamon, baking powder, baking soda, salt, and nutmeg. In a large bowl, mix together the applesauce, eggs, coconut oil, honey, and vanilla. Add half of the flour mixture; stir. Add the Greek yogurt; stir. Add the remaining flour mixture; stir until just blended.
Divide batter between muffin pans by filling each muffin cup approximately 2/3 full with batter. Bake for 14 to 18 minutes, or until a toothpick inserted in the center of a muffin comes out clean. Cool in the pans for a few minutes before turning out onto wire rack to cool completely.
Whole wheat pastry flour is the key to 100% whole wheat muffins that aren't heavy and dense. Whole wheat pastry flour lends baked goods a nice, light texture — more akin to that of using white flour — but with the wholesome nutritional benefits of 100% whole wheat. If you can't find whole wheat pastry flour, you may substitute half white flour and half regular whole wheat flour...but the muffins won't turn out quite the same and they won't be 100% whole wheat.
These muffins turn out best when all ingredients are at room temperature. If my applesauce is refrigerated, I set it out ahead of time along with the measured-out 1/2 cup of Greek yogurt. To quickly warm up cold eggs, I put them in a bowl of warm water for a few minutes.
Sometimes I fill my muffin cups a little fuller and only end up with 22 or 23 muffins...that's okay, too. ;)
OPTIONAL STREUSEL TOPPING: In a small bowl, combine 2/3 cup brown sugar, 1 cup rolled oats, and 1 teaspoon cinnamon. Using a fork or your fingers, work in 4 tablespoons softened butter (I prefer salted, but unsalted will work) until crumbly. Sprinkle over the tops of the muffins before baking as directed.