Healthy Pumpkin Chocolate Chip Muffins {Freezer Meal}

These healthy Pumpkin Chocolate Chip Muffins are moist, sweet, and delicious…and easily freezable. We pull them out of the freezer for snacks or for an easy breakfast.

Pumpkin Chocolate Chip MuffinsIt’s the time of year when everyone wants a little pumpkin in their life. These healthy Pumpkin Chocolate Chip Muffins are moist, sweet, and delicious…and easily freezable.  We make them every other week and pull them out of the freezer for snacks or breakfast. Enjoy!

pumpkin chocolate chip muffins in a basket


Pumpkin Chocolate Chip Muffins

  • Author: Thriving Home
  • Prep Time: 20 mins
  • Cook Time: 20 mins
  • Total Time: 40 mins
  • Yield: 24 mini muffins


Healthy pumpkin chocolate chip muffin recipe. So delicious and at the same time, nutritious! Try them regular-sized or as mini muffins.


  • 1 cup all-purpose flour (I use white whole wheat flour for this)
  • 1/2 cup whole wheat flour
  • 1/4 cup ground flaxseed or wheat germ
  • 2 teaspoons baking powder
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon real salt
  • 1 cup of pureed pumpkin (canned pure pumpkin is what I use)
  • 2 large eggs, beaten
  • 1/2 cup packed brown sugar
  • 1/2 cup 1% lowfat milk
  • 1/3 cup oil (I use melted coconut oil)
  • 1 teaspoon real vanilla
  • 1/2 cup mini chocolate chips (or dark chocolate chips)


  1. Preheat the oven to 350°F. Lightly oil or coat a 24-cup mini muffin tin or a 12-cup regular-sized muffin tin with nonstick cooking spray and set aside.
  2. In a mixing bowl, whisk together the flours, ground flaxseed, baking powder, cinnamon, and salt.
  3. In another bowl, whisk together the pumpkin, eggs, brown sugar, oil, milk, and vanilla and stir until well combined.
  4. Pour the liquid ingredients into the dry ingredients and stir until just moistened. Stir in the chocolate chips.
  5. Spoon the batter into the prepared muffin cups. Bake mini muffins for 15-17 minutes or 12 full-size muffins for 18-20 minutes, until a toothpick inserted in the center comes out clean. Transfer the pan to a wire rack and cool 5 minutes. Remove the muffins and cool an additional 5 minutes before serving.


To Freeze: Bake and cool completely. Place muffins in a single layer in a gallon-sized freezer bag, squeeze out the air, and seal. Freeze.

To Prepare From Frozen: Let a muffin sit on the counter for a few minutes or use the defrost setting to thaw.

Close up of pumpkin chocolate chip muffins in a basket

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  1. Maria says

    Do you have the nutritional info/calorie count for these, by chance?

    • Polly says

      Sorry, Maria. We don’t (yet) provide the nutritional information on our recipes.

  2. Len says

    Also, could you substitute anything for the pumpkin? Banana maybe, I have a ton I need to get rid of, thanks so much!

    • Rachel says

      I have found you can sub many different pureed or mashed up veggies or fruit, including bananas, squash, sweet potato, or applesauce. You may want to cut back a little on the sugar if you’re using all bananas, since it will add more sweetness.

  3. Len says

    Can you use all white flour? I have all of the ingredients except for whole wheat flour. I was thinking I could use 1½cups of white flour?

    • Rachel says

      Yes, I think that would be fine.

  4. Mallory Decker says

    Do you freeze the muffins before or after you bake them?

    • Rachel says

      Yes, you freeze after they are baked and cooled.

  5. debbie says

    What size pumpkin? Around here it comes in 15 and 30 ounce cans….

    • Rachel says

      It doesn’t really matter, as long as you have 1 cup (not one can). 🙂

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  7. Patti says

    Sound yummy! Will definitely have to try these!!

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  9. Peg T says

    Do you think these would still taste good if you did not add the brown sugar?

    • Rachel says

      Hmm, not in my opinion. The chocolate chips don’t add enough sweetness without the sugar. You could try some stevia powder or liquid (no calories, all-natural and very sweet, but has a distinct taste) if you’re wanting to cut out sugar.

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