In a large mixing bowl, whisk together whole wheat flour, baking powder, baking soda, 1 teaspoon cinnamon, nutmeg, and salt until well combined.
In a medium bowl, whisk together coconut sugar and melted coconut oil until smooth. Add Greek yogurt, eggs (one at a time), almond milk, and vanilla extract, whisking until completely combined and smooth.
Pour the wet ingredients into the dry ingredients and gently fold together using a rubber spatula until just combined. Do not overmix - a few lumps are perfectly fine.
Gently fold in the cinnamon-coated apple pieces, distributing them evenly throughout the batter.