Chocolate Pumpkin Zucchini Muffins – Fit Foodie Finds


Get the best of both worlds with these incredibly moist chocolate pumpkin zucchini muffins. We created 1 base batter with zucchini and pumpkin and removed a little of it and mixed in cocoa powder to get that zucchini chocolate + pumpkin swirl.

chocolate pumpkin zucchini muffins on a cooling rack

When you can’t choose between chocolate pumpkin muffins and zucchini muffins, swirl them together for one epic flavor! We love the array of flavors this muffin provides, it truly screams fall.

This recipe is made with white whole wheat flour and coconut sugar, but we also tested it with all-purpose flour and brown sugar to make it more accessible. We definitely found that if you do use white whole wheat flour, they will be a bit denser thanks to the whole grains.

What You Need for these Muffins

The base of these muffins is made from white whole wheat flour, eggs, pumpkin puree, shredded zucchini, brown sugar, and maple syrup. You’ll also need cocoa powder, coconut oil, and almond milk.

how to remove the moisture from shredded zucchini


  • Add-ins: feel free to add chopped nuts or shredded coconut to give these more pizzaz.
  • Loaf: turn it into a loaf by swirling the pumpkin layer on top of the chocolate in a standard loaf pan. Bake at 350ºF for 50-60 minutes or until fully cooked.
  • Make it g/f: use a gluten-free flour blend in place of normal flour.
how to swirl muffins with pumpkin and chocolate

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.

chocolate pumpkin zucchini muffins cut in half to show the swirl

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.

More Zucchini Recipes

chocolate pumpkin zucchini muffins on a cooling rack

More Muffin Recipes

chocolate pumpkin zucchini muffins on a cooling rack

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:20 minutes

Cook:20 minutes

Total:40 minutes


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


  • 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.

Tips & Notes

  • This recipe yields 14 muffins, requiring 2 muffins to be baked separately if your muffin tin yields the traditional 12 muffins.
  • Don’t forget to remove the moisture from your 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.

Nutrition facts

Calories: 195kcal Carbohydrates: 31g Protein: 4g Fat: 7g Fiber: 3g Sugar: 19g


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