Preheat the oven to 350 degrees Fahrenheit and place a rack in the middle of the oven. Line 12 muffin insertions with liners or lay a silicone muffin tray on a baking sheet.
In a large bowl, combine the almond flour, oats, spelt flour, cinnamon, baking powder and ground flax. Stir to combine.
In a separate bowl, whisk together the eggs, the vanilla extract, the maple syrup and the coconut oil.
Make a hole in the center of the dry ingredients and pour the wet ingredients into the middle. Mix with a fork until just combined.
Stir-in the pecans, grated carrot and grated apple. Divide the mixture evenly among the 12 muffin insertions.
Bake the muffins for 20 to 25 minutes, until golden brown.
Notes
Freezing instructions: Allow muffins to cool down to room temperature. Freeze muffins for an hour or until solid. Transfer the frozen muffins to a freezer-safe bag, remove excess air and store for up to two months. To reheat, remove the muffin from the freezer and heat in the microwave or oven until warm.