Preheat oven to 350ºF. Prepare muffin tin with 12 paper liners, and spray liners with nonstick cooking spray.
In a large bowl, whisk together the almond flour, salt, baking soda and cinnamon. Set aside.
Place the apples, coconut oil, honey, eggs and vanilla in the bowl of a food processor and blend until fairly smooth. Pour the apple mixture into the bowl with the almond flour and stir until well combined. Fold in pecans and caramel bits. Spoon batter into prepared muffin pan.
Bake the muffins in a 350°F oven for 25 to 30 minutes or until golden brown and a tooth pick inserted into the center comes out clean. Allow to cool in the pan for 10 minutes and then transfer to a wire rack to cool completely.
Muffins can be stored in an airtight container at room temperature for up to 3 days.