Chocolate Pumpkin Zucchini Muffins

These Chocolate Pumpkin Zucchini Muffins pack the most delicious combination of Fall flavors. An easy recipe to double or triple and freeze for later, make a batch of these muffins today!

Muffins, muffins everywhere! Whether you’re about to whip up a batch of these chocolate pumpkin zucchini muffins or these super fluffy blueberry muffins or these whole grain carrot cake muffins, you’ll never run out of delicious muffin recipes here on Fit Foodie Finds.

chocolate pumpkin zucchini muffins on a cooling rack

Zucchini + Muffins = A Match Made in Heaven

Seriously, we can’t get enough of baking with zucchini this fall. It seems like everyone is gifting their garden zucchini, and there’s only so much zucchini cooking one can do. Which leads us to these delicious chocolate pumpkin zucchini muffins!

How to Remove Moisture from Zucchini

Once you shred your zucchini, simply place it into a paper towel and wring out the moisture over the sink. You’ll be surprised how much moisture shredded zucchini actually holds! This is a crucial step as it will prevent your zucchini muffins from being overly moist / soggy.

how to remove the moisture from shredded zucchini

How to Swirl Muffins

What an easy way to fancy up your chocolate pumpkin zucchini muffins! Mix up your batter per the recipe instructions, adding everything except the cocoa powder. Once you have everything except the cocoa powder mixed thoroughly, remove 1 cup of batter from the bowl.

Then, add cocoa powder to the remaining batter, and stir together completely before scooping into the muffin tins. Fill each muffin cup equally, and then spoon in AMOUNT OF BATTER of the non-cocoa batter to the top of each muffin cup and then swirl with a toothpick.

how to swirl muffins with pumpkin and chocolate

How to Freeze Muffins

If you have as many zucchini on hand right now as we do, this is a great recipe to make a double or triple batch and then freeze for later enjoyment throughout the fall months. It’s super easy:

  1. First, let the muffins cool completely.
  2. Then, place muffins on a baking sheet and place the baking sheet into the freezer.
  3. Freeze for at least 2 hours.
  4. Once the muffins are frozen, transfer into a freezer-safe, gallon-size bag. Then, remove as much air as possible and seal.
  5. Write “Chocolate Pumpkin Zucchini Muffins” on the front of the bag along with an “eat by date” 3 months from the time you made the muffins.

To thaw: remove a frozen muffin from the bag. Then, let thaw on the countertop for 30 minutes OR defrost in the microwave for a few minutes, and enjoy.

chocolate pumpkin zucchini muffins cut in half to show the swirl

More Zucchini Recipes

chocolate pumpkin zucchini muffins on a cooling rack

More Muffin Recipes


Chocolate Pumpkin Zucchini Muffins

These Chocolate Pumpkin Zucchini Muffins pack the most delicious combination of Fall flavors. An easy recipe to double or triple and freeze for later, make a batch of these muffins today!

  • Prep Time: 20 minutes
  • Cook Time: 20 minutes
  • Total Time: 40 minutes
Author: Lee Funke
Yield: 14 1x
Category: Muffins
Method: Oven
Cuisine: American


Dry Ingredients

  • 1.5 cups white whole wheat flour
  • ½ cup coconut sugar
  • 1 cup shredded zucchini (moisture removed)
  • 1 teaspoon baking soda
  • 1/8 teaspoon salt
  • 1/2 cup cocoa powder
  • 1/2 cup semi-sweet chocolate chips

Wet Ingredients

  • 2 large eggs
  • 1/2 cup maple syrup
  • 1 cup unsweetened almond milk, separated (3/4 cup and 1/4 cup)
  • 1 cup unsweetened pumpkin puree
  • 3 tablespoons coconut oil, melted


  1. First, preheat oven to 350ºF and line a muffin tin with muffin liners. We suggest also spraying your muffin liners with cooking spray just in case.
  2. Next, place dry ingredients (except for the cocoa powder and chocolate chips) into a medium bowl  and mix.
  3. Then, in a large bowl crack 2 eggs and whisk. Add maple syrup, 3/4 cup almond milk, and pumpkin puree and mix again.
  4. Add dry ingredients to wet ingredients and mix. Then, add in melted coconut oil and mix again.
  5. Remove 1/2 cup of muffin batter without cocoa powder from the bowl. Set it aside for later.
  6. Finally, add the cocoa powder, chocolate chips, and the last 1/4 cup of almond milk to the bowl. Mix well until combined.
  7. Fill each muffin cup about 3/4 of the way full with the chocolate batter. Then, scoop 1 teaspoon of the non-chocolate muffin batter on top of each muffin.
  8. Take a toothpick or knife and swirl the two layers together.
  9. Then, place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
  10. Let cool for 5 minutes and then remove from the muffin tin to continue cooling.


This recipe yields 14 muffins, requiring 2 muffins to be baked separately if your muffin tin yields the traditional 12 muffins.


  • Serving Size: 1 muffin
  • Calories: 195
  • Sugar: 19
  • Sodium: 133
  • Fat: 7
  • Carbohydrates: 31
  • Fiber: 3
  • Protein: 4
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