Preheat and prep: Heat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or lightly grease it.
Mix dry ingredients: In a large bowl, whisk together whole wheat flour, oats, ground flaxseed, baking powder, baking soda, salt, cinnamon, and nutmeg.
Mix wet ingredients: In a separate bowl, whisk the Greek yogurt, applesauce, milk, eggs, maple syrup, vanilla, and oil until smooth.
Combine: Pour the wet ingredients into the dry. Stir gently with a spatula until just combined. Do not overmix; a few streaks of flour are okay.
Add-ins: Fold in your chosen fruit, nuts, or extras.
If using juicy fruit like blueberries, toss them with a teaspoon of flour first to help prevent sinking.
Fill the pan: Divide the batter evenly among the muffin cups. They should be about ¾ full. Sprinkle with oats or seeds if you like.
Bake: Place on the middle rack and bake for 16–20 minutes, or until the tops are set and spring back lightly.
A toothpick should come out with a few moist crumbs, not wet batter.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps set the crumb and prevents soggy bottoms.