Preheat oven to 375 degrees F (190 degrees C). Place cupcake liners in 18 muffin cups.
Mix rolled oats, coconut flour, baking soda, baking powder, cinnamon, nutmeg, cloves, and salt together in a bowl.
Mix applesauce, pumpkin puree, almond milk, eggs, coconut oil, agave nectar, and vanilla extract together in a separate bowl until thoroughly blended. Add flour mixture and stir just until flour is incorporated into the batter, about 1 minute. Fill muffin cups evenly with batter.
Bake in preheated oven until a toothpick inserted into a muffin comes out clean, 20 to 25 minutes.