Preheat oven to 325 degrees F, and prepare a muffin tin with parchment paper or muffin liners.
In a medium mixing bowl, combine the almond flour, tapioca starch, cinnamon, nutmeg, ground ginger, ground cloves, baking soda and salt. Whisk together until well combined.
In a separate medium mixing bowl, combine the eggs and coconut sugar with a hand mixer. Add the canned pumpkin, almond milk, vanilla and coconut oil, and mix until well combined.
Add the dry ingredients into the wet ingredients, and use hand mixer to combine.
Add chopped sage and mix to combine.
Divide batter evenly between 12 muffin tins, then top evenly with the pecan crumble mixture. Lightly press the crumble into the muffin batter.
Bake at 325 degrees F for 25 minutes, or until a toothpick comes out clean and the crumble is lightly browned on top.