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.
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 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 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:
- First, let the muffins cool completely.
- Then, place muffins on a baking sheet and place the baking sheet into the freezer.
- Freeze for at least 2 hours.
- Once the muffins are frozen, transfer into a freezer-safe, gallon-size bag. Then, remove as much air as possible and seal.
- 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.
More Zucchini Recipes
- Grilled Zucchini
- Healthy Zucchini Bread
- Zucchini Lasagna
- Whole Wheat Zucchini Chocolate Chunk Waffles
- 25 Healthy Zucchini Recipes
More Muffin Recipes
- Super Fluffy Blueberry Muffins
- Whole Grain Blender Breakfast Muffins
- Whole Grain Carrot Cake Muffins
- Healthy Chocolate Muffins
- 6 Healthy Muffin Recipes (One Base Batter)

Chocolate Pumpkin Zucchini Muffins
Ingredients
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
Instructions
- 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.
- Next, place dry ingredients (except for the cocoa powder and chocolate chips) into a medium bowl and mix.
- Then, in a large bowl crack 2 eggs and whisk. Add maple syrup, 3/4 cup almond milk, and pumpkin puree and mix again.
- Add dry ingredients to wet ingredients and mix. Then, add in melted coconut oil and mix again.
- Remove 1/2 cup of muffin batter without cocoa powder from the bowl. Set it aside for later.
- Finally, add the cocoa powder, chocolate chips, and the last 1/4 cup of almond milk to the bowl. Mix well until combined.
- 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.
- Take a toothpick or knife and swirl the two layers together.
- Then, place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
- Let cool for 5 minutes and then remove from the muffin tin to continue cooling.
Is the nutrition facts for the whole batter, or per muffin??
Would it be possible to add protein powder to these?
These were SO yummy! I’ve never met a muffin recipe I didn’t love on FFF. Mine ended up making much more muffins than what was listed, but that’s never a bad thing! I made 12 regular sized muffins (a little small) + 12 mini muffins!
Heck yes! Glad you got a few extras, too 😛
Can I use all purpose flour and regular white granulated sugar?