Preheat oven to 325 degrees Fahrenheit (165 degrees Celsius) and grease a standard 12-cup muffin tin with non-stick spray or liners.
In a large mixing bowl, whisk together the whole wheat flour, baking soda, salt, cinnamon, ginger, nutmeg, and cloves until well aerated.
In a separate medium bowl, whisk together the melted coconut oil and maple syrup until combined.
Add the eggs to the oil mixture and whisk vigorously until emulsified.
Incorporate the pumpkin puree, almond milk, and vanilla extract into the wet mixture, stirring until smooth.
Fold the wet ingredients into the dry ingredients using a spatula, stirring until just combined to avoid overworking the gluten.
Distribute the batter evenly across the prepared 12 muffin cups.
Bake for 22 to 25 minutes, or until a skewer inserted into the center of a muffin comes out clean.
Transfer the muffin tin to a wire rack to cool for 5 minutes before removing individual muffins.