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 Muffins

It’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
  • Yield: 24 mini muffins or 12 regular muffins 1x


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
  • ½ cup whole wheat flour
  • ¼ cup ground flaxseed
  • 2 teaspoons baking powder
  • ½ teaspoon cinnamon
  • ¼ teaspoon salt
  • 1 cup canned pure pumpkin
  • 2 large eggs, beaten
  • ½ cup packed brown sugar
  • ½ cup milk (your choice)
  • 1/3 cup avocado oil or melted coconut oil
  • 1 teaspoon real vanilla
  • ½ cup mini chocolate chips


  1. Preheat the oven to 350°F. Lightly oil or coat a mini muffin tin or regular-sized muffin tin with nonstick cooking spray and set aside.
  2. In a large bowl, whisk together the flours, ground flaxseed, baking powder, cinnamon, and salt. In a medium bowl, stir together the pumpkin, eggs, brown sugar, oil, milk, and vanilla until well combined. Pour the liquid ingredients into the dry ingredients and stir just until moistened. Stir in the chocolate chips.
  3. Spoon the batter into the prepared muffin cups. Bake 15-18 minutes for mini muffins or 20-23 minutes for regular-sized muffins, or until a toothpick inserted in the center comes out clean. Let muffins cool on a wire rack. (Freezing instructions begin here.)


Freeze For Later: Bake muffins and cool completely. Place muffins in a single layer in a gallon-sized freezer bag or container, seal, and freeze. Prepare From Frozen: Let a muffin sit on the counter for a few minutes or use the defrost setting on the microwave to thaw.

Close up of pumpkin chocolate chip muffins in a basket

Want More Pumpkin Recipes?

With YEARS worth of content and recipes on Thriving Home, it can be easy to forget about some amazing pumpkin recipes that we have shared over the years. Here are our Top 10 Pumpkin Recipes that you simply must try!

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  1. Elinor says

    These are so good!! I used olive oil and butternut squash and omitted cinnamon and salt.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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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  8. Patti says

    Sound yummy! Will definitely have to try these!!

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  10. 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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