Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease each cup.
In a large bowl, whisk together whole wheat flour, baking soda, salt, cinnamon, nutmeg, ginger, and cloves. This ensures even distribution of flavors.
In another bowl, whisk together pumpkin puree, honey (or maple syrup), eggs, melted coconut oil, almond milk, and vanilla extract until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined. Avoid overmixing, as this can make the muffins dense. If using mix-ins like nuts, chocolate chips, or dried fruit, fold them in at this stage.
Spoon the batter evenly into the prepared muffin cups, filling each about ¾ full.
Place the muffin tin in the preheated oven and bake for 18–22 minutes, or until a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely. Enjoy warm or at room temperature!