Preheat your oven to 350ºF (175ºC). Line a muffin tin with muffin liners to prevent sticking. For extra assurance, lightly spray the liners with cooking spray. This helps the muffins release more easily once they're baked.
In a medium bowl, mix together the flour, brown sugar, baking soda, and salt. Set aside the cocoa powder and chocolate chips for later. Give the mixture a quick stir to ensure the leavening and salt are well distributed.
In a large bowl, crack in the eggs and whisk until combined. Add the maple syrup, 3/4 cup of the almond milk (reserve the remaining 1/4 cup for later), and pumpkin puree. Whisk everything together until smooth.
Add the dry ingredient mixture from Step 2 to the wet ingredient mixture from Step 3. Mix gently until just combined; be careful not to overmix. Next, stir in the melted coconut oil and the shredded zucchini (make sure its moisture has been removed) until well incorporated.
Remove 1/2 cup of the plain muffin batter and set it aside in a small bowl—this will be used for a swirl on top. To the remaining batter, add the cocoa powder, chocolate chips, and the reserved 1/4 cup almond milk. Mix thoroughly until the cocoa is fully blended and the chips are distributed evenly throughout the batter. I like to use good-quality cocoa powder for a richer chocolate flavor.
Fill each muffin cup about 3/4 full with the chocolate batter. Then, top each muffin with about 1 teaspoon of the reserved plain batter from earlier. Use a toothpick or knife to gently swirl the two batters together to create a marbled effect.
Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted in the center comes out clean. Let the muffins cool in the tin for about 5 minutes, then transfer them to a wire rack to finish cooling. For extra moist muffins, I recommend not overbaking them—check them around 18 minutes and add more time only if needed.