Name: Healthy Chocolate Pumpkin Muffins
Prep time: 15 min
Cook time: 22 min
Total time: 42 min
Yield: 12 muffins
Cuisine: American
Ingredients: 1 cup pumpkin puree (not pumpkin pie filling); 2 large eggs; 1/3 cup pure maple syrup; 1/4 cup coconut oil (melted and slightly cooled); 1 tsp vanilla extract; 1 cup whole wheat pastry flour; 1/3 cup unsweetened cocoa powder; 1 tsp baking soda; 1 tsp cinnamon; 1/2 tsp pumpkin pie spice; 1/4 tsp fine sea salt; 1/2 cup dark chocolate chips (plus more for topping)

Jump to Recipe

My kids demolished a full batch before I could photograph them, which told me everything I needed to know.

Pumpkin puree keeps these moist for days, cocoa handles the depth, and the whole thing comes together in one bowl before your oven even finishes preheating.

Fudgy, spiced muffins that taste like dessert and actually have something to show for themselves nutritionally.

4.7 (100 reviews)

Vegetarian

Prep15 min

Cook22 min

Cool in pan5 min

Total42 min

Serves12 muffins

Ingredients

1 cup pumpkin puree , not pumpkin pie filling
2 large eggs
1/3 cup pure maple syrup
1/4 cup coconut oil , melted and slightly cooled
1 tsp vanilla extract
1 cup whole wheat pastry flour
1/3 cup unsweetened cocoa powder
1 tsp baking soda
1 tsp cinnamon
1/2 tsp pumpkin pie spice
1/4 tsp fine sea salt
1/2 cup dark chocolate chips , plus more for topping

Instructions

Heat your oven to 350 degrees F and line a 12-cup muffin tin with paper liners. The liners matter here because these are moist muffins and they will stick to an ungreased pan.

Whisk the pumpkin puree, eggs, maple syrup, melted coconut oil, and vanilla together in a large bowl until the mixture looks glossy and fully combined, about 45 seconds.

Add the flour, cocoa powder, baking soda, cinnamon, pumpkin pie spice, and salt directly to the wet ingredients. Stir with a spatula until just combined, stopping the moment you no longer see dry streaks. The batter will be thick and smell like brownie mix. Do not overmix or the muffins will bake up dense.

Fold in the chocolate chips with 3 or 4 slow turns of the spatula.

Divide the batter evenly among the 12 cups, filling each about three-quarters full. Press a few extra chocolate chips onto the top of each muffin so they look intentional when they come out.

Bake for 20 to 22 minutes. At 20 minutes, press the center of one muffin gently with your fingertip. It should spring back firmly and not feel wet or sunken. A toothpick inserted in the center should come out with a few moist crumbs, not wet batter.

Let the muffins cool in the pan for 5 minutes. You will hear them pulling slightly away from the liners as they settle. Turn them out onto a wire rack. They firm up as they cool and the chocolate smell intensifies once they hit the air.

Tips & Notes

Use a cookie scoop to portion the batter so all 12 muffins bake evenly and finish at the same time.
If your coconut oil is hot when it hits the eggs it will scramble them. Give it 5 minutes on the counter after melting before you start mixing.
Whole wheat pastry flour keeps the texture light. Regular whole wheat flour will make these noticeably denser, which is fine but different.
These are best the day after baking once the spices have had time to settle into the crumb.

Storage: Store in an airtight container at room temperature for up to 3 days, or refrigerate for up to 6 days. Freeze individually wrapped muffins for up to 2 months and thaw overnight at room temperature.

Nutrition per serving · estimated

178 Cal

8g Fat

25g Carbs

4g Protein

3g Fiber

11g Sugar

160mg Sodium

-13%

Why Pumpkin and Cocoa Actually Work Together

Pumpkin puree has almost no flavor on its own, which sounds like a problem but is actually the whole point. It adds moisture and body without competing with the cocoa, so you get a fudgy crumb without needing butter or oil in large quantities.

The spices bridge the two. Cinnamon and pumpkin pie spice read as warm and earthy, which lands somewhere between chocolate cake and a spiced fall muffin. It is not a compromise. It is its own thing.

Swaps That Have Worked in My Kitchen

Almond flour does not work here as a straight swap. I tried it twice and both times the muffins collapsed in the center. If you need gluten-free, a 1-to-1 gluten-free baking flour holds up fine.

Honey works in place of maple syrup in equal amounts, though the flavor is slightly more floral. Avocado oil works in place of coconut oil with no noticeable difference in texture or taste.

Healthy Chocolate Pumpkin Muffins