Preheat your oven to 350 degrees F. This is an essential step to ensure your muffins rise properly. While the oven is heating, line a 12-cup muffin tin with liners and spray the inside of the liners with nonstick cooking spray to prevent sticking.
In a large mixing bowl, combine pumpkin puree, maple syrup, eggs, almond milk, and vanilla extract. Mix them together until you have a smooth and creamy texture. This mixture is your wet ingredients, and it should smell wonderfully fragrant already!
In a separate large bowl, whisk together the dry ingredients: whole wheat pastry flour, baking soda, cinnamon, nutmeg, ginger, allspice, and salt. Whisking well is important to ensure that the leavening agent is evenly distributed throughout the flour.
Once combined, add the dry ingredients to the wet ingredients and mix until just combined. Be careful not to overmix; a few lumps are perfectly fine! Next, gently stir in the melted coconut oil, which adds richness to your muffins.
Now, divide the batter in half. Transfer half of the batter to a separate medium bowl. In this bowl, stir in the cocoa powder and ¼ cup of chocolate chips. Mix until just combined, creating your chocolate batter.
Take your prepared muffin tin and start by spooning less than 1 tablespoon of the pumpkin batter into each muffin liner. Then, add 1 tablespoon of the chocolate batter on top of the pumpkin batter. Repeat this process until all of your batter is used. The goal is to create lovely layers!
With a knife, gently swirl the batters together about 3 to 4 times to create a marbled effect. Don’t overdo it; you want to maintain that beautiful swirled look!
Give your muffin pan a gentle shake back and forth to even out the batter in each cup. Then, sprinkle the remaining chocolate chips on top of the batter for extra chocolatey goodness.
Pop the muffin tin into the oven and bake for 20 to 25 minutes. Keep an eye on them; I find that 22 minutes usually does the trick! They’re done when a tester inserted into the center comes out clean.
Once baked, allow the muffins to cool in the pan for 10 minutes before transferring them to a wire rack. This allows them to firm up nicely before you dig in!