Preheat the Oven
Preheat oven to 350°F. Line a 12-cup muffin pan with paper liners or spray with nonstick cooking spray.
Mix Dry Ingredients
In a large mixing bowl, whisk together almond flour, quick oats, ground flaxseed, chia seeds, cinnamon, baking powder, baking soda, and kosher salt for about 30 seconds until well combined.
Combine Wet Ingredients
In a second bowl, whisk eggs until blended and slightly frothy. Add melted coconut oil (cooled), Greek yogurt, honey, and vanilla extract. Whisk until smooth and creamy with no streaks visible, about 1 minute.
Create the Muffin Batter
Pour wet ingredients into the bowl with dry ingredients. Using a rubber spatula, gently fold together with broad strokes just until dry ingredients are moistened. Do not overmix - some small lumps are fine.
Add the Apples
Grate apples using the large holes of a box grater, leaving skin on. Place grated apple in a clean kitchen towel and squeeze gently to remove excess liquid. Measure 1 packed cup. Fold grated apple into batter gently but thoroughly until evenly distributed.
Fill the Muffin Cups
Using a large spoon or ice cream scoop, divide batter evenly among muffin cups, filling each about three-quarters full.
Bake the Muffins
Place muffin pan in center of preheated oven. Bake for 20-22 minutes, until a toothpick inserted in the center comes out clean and tops are golden brown with slightly cracked surfaces.
Cool the Muffins
Let muffins cool in pan for 15 minutes, then transfer to a wire rack to cool completely.