Preheat the oven to 175 degrees Celsius (350 degrees Fahrenheit)
Start by making the apple puree. In a pot on medium low heat simmer the apples in water for approx 10-15 minutes or until all of the water has evaporated and the apples are soft. Once cooked using a potato masher or fork, roughly smash the apples until they form a chunky puree.
Peel and core approximately 2 small apples. Using a cheese grater, grate the apples to equal 1 cup.
In a mixing bowl combine the almond flour, eggs, coconut oil, nutmeg, cinnamon, baking soda, apple puree, honey and salt. Once completely combined add in the shredded apple as well as 3 tablespoons of the chopped pecans. Stir.
Line a large muffin tray with paper cups and fill each with batter. This should make approximately 9-10 muffins.Sprinkle the top of each muffin with the remaining chopped pecans.
Bake in the oven for approximately 20-25 minutes until a toothpick inserted into the muffins comes out clean