Pumpkin Chocolate Chip Muffins

By Rachel Tiemeyer
September 29, 2021

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.

Note from 9/2021: We retested, tweaked, and updated this older recipe. They are now more nutritious and tastier than before!

pumpkin chocolate chip muffins in a muffin tin on a cooling rack

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It’s the time of year when everyone wants a little pumpkin in their life, but I make these muffins year round.  My kids LOVE them, so I double and freeze them for snacks and breakfasts regularly.

INGREDIENTS IN OUR HEALTHY PUMPKIN CHOCOLATE CHIP MUFFINS

What makes this recipe more nutritious than most (yet still moist and delicious)? Well, here’s the line-up of ingredients…

hand holding a pumpkin chocolate chip muffin that's broken in half to show the interior
  • White whole wheat flour – Note the name of this is WHITE whole wheat flour, which is a special variety that you can now find in most grocery stores. I love baking with this 100% whole grain flour, because it’s lighter than usual store-bought whole wheat (known as the red wheat variety). It’s a great swap out for all purpose flour.
  • Ground flaxseed – This ground seed packs in omega 3 fatty acids and fiber that we can all use more of. Be sure to store in the fridge or freezer to give it a longer shelf life. Read more about the health benefits here.
  • Sugar – You need some sugar to make these irresistible, but I like to use coconut sugar as a bit healthier alternative. You can also reduce the amount of a sugar by 1/4 cup and still have some pretty darn tasty muffins.
  • Cinnamon – Because pumpkin and cinnamon need each other in baked goods. (It’s a healthy co-dependent relationship, I tell you.)
  • Salt – A little salt in baked goods helps balance out the sweetness.
  • Unsweetened applesauce – For a little more moisture and all natural sweetness. You can substitute in more pureed pumpkin for this, if you like.
  • Large eggs – Three eggs add a lot of protein to these muffins and help give them “lift”. I usually look for organic eggs from a local farmer, if I can find them.
  • Avocado oil – If you’ve been around Thriving Home for long, you know we love this neutral cooking/baking oil with a high smoking point. The healthiest version is the extra virgin avocado oil, because there are no chemical solvents used in the processing. Read more about it here.

HOW TO MAKE PUMPKIN CHOCOLATE CHIP MUFFINS

This recipe is so easy that your kids can help you or even make these themselves as they get older.

STEP 1: PREPARE THE OVEN AND PAN

Preheat the oven to 350°F. Grease 18-20 muffin cups or line them with paper liners. (You can make two batches back to back, if you only have one 12-cup muffin tin.)

STEP 2: MIX DRY INGREDIENTS

In a large mixing bowl, combine the flour, flax, sugar, baking soda, baking powder, cinnamon, and salt.

dry ingredients for muffins in a glass bowl with whisk

STEP 3: MIX WET INGREDIENTS

In another mixing bowl, stir together the pumpkin puree, oil, applesauce, eggs, and vanilla extract.

Wet ingredients for muffins in a glass bowl with whisk in it

STEP 4: COMBINE THE DRY AND WET INGREDIENTS

Stir the wet mixture into dry ingredients. Like most muffin recipes, it’s important to mix the wet and dry ingredients separately and then combine just until it comes together. If you over mix the batter, the gluten will develop stronger bonds and make the muffins tough. Lastly, gently stir in the chocolate chips.

muffin batter with chocolate chips in a mixing bowl with wooden spoon

STEP 5: FILL THE MUFFIN TIN

Spoon the batter into the prepared muffin tins until each one is almost full–about 2-3 heaping tablespoons full. I use a small cookie dough scooper, but a spoon works just fine. You may want to wet your fingers to help the batter slip off the spoon.

pumpkin chocolate chip Muffin batter being scooped into a muffin tin

STEP 6: BAKE AND COOL

Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 18-20 minutes. Place on a cooling rack for 10 minutes or so. Then remove the muffins and let them cool even more on the rack.

pumpkin chocolate chip muffins in a tin on a cooling rack

HOW TO FREEZE PUMPKIN MUFFINS

You know how much we love prepping foods and meals that can freeze for later. As we always say, the key is freezing anything the RIGHT way so that it comes out tasting fresh. Here’s how to freeze these muffins the best way:

  • Bake as directed.
  • Let them cool completely. This is super important!
  • Place them in a gallon-sized freezer bag and seal tightly–squeezing out as much air as humanely possible. Reducing air exposure to the muffins is crucial to maintaining good texture. Tip: If you really want them to last a long time, wrap each one individually in plastic wrap first. But, I’d just suggest eating them quickly instead of going through that trouble, ha!
  • Store in the back of the freezer for up to 3 months.

Read this entire post on how to store and freeze muffins for more info!

CAN I MAKE THESE MUFFINS DAIRY-FREE OR GLUTEN-FREE?

It’s incredibly easy to make these dairy-free. The only ingredient that has dairy in it would be the chocolate chips. Simply leave them out or use dairy-free chocolate chips like Enjoy Life brand

If you want a gluten-free pumpkin muffin, be sure to try my gluten-free Coconut Flour Pumpkin Muffins. Don’t worry, they still have chocolate chips in them and are super moist and delicious, too!

Pumpkin Muffins with Chocolate Chips stacked on a white plate

OTHER TASTY PUMPKIN RECIPES TO TRY

If you’re a lover of all things pumpkin, then be sure to try some of these other favorite baked goods on our site.

Everyone in our family gave these healthier pumpkin muffins two thumbs up. I hope you enjoy them, too.

Print

Pumpkin Chocolate Chip Muffins

  • Author: Thriving Home
  • Prep Time: 15 minutes
  • Cook Time: 18 minutes
  • Total Time: 33 minutes
  • Yield: 1820 muffins 1x
  • Category: Breakfast
  • Method: Bake
  • Diet: Vegetarian

Description

These healthier pumpkin muffins are moist, sweet, and delicious…and easily freezable. We pull them out of the freezer for snacks or for an easy breakfast.


Ingredients

  • 2 1/2 cups white whole wheat flour (sub: 1 1/2 cups whole wheat + 1 cup all purpose flour)
  • 1/2 cup ground flaxseed (sub: oats)
  • 1 cup sugar (use coconut sugar for a healthier alternative)
  • 2 teaspoons baking soda
  • 1 teaspoon baking powder (I like this aluminum-free kind.)
  • 2 teaspoons cinnamon
  • 1/2 teaspoon salt
  • 1 1/2 cups (or one 15 ounce can) pumpkin puree
  • 2/3 cup avocado oil or melted coconut oil
  • 1/2 cup unsweetened applesauce
  • 3 large eggs
  • 1 teaspoon pure vanilla extract
  • 1 cup semi sweet chocolate chips

Instructions

Make It Now:

  1. Preheat oven to 350°F. Grease 18-20 muffin cups or line them with paper liners. 
  2. In a large mixing bowl, combine the flour, flax, sugar, baking soda, baking powder, cinnamon, and salt.
  3. In a smaller bowl, whisk together the pumpkin puree, oil, applesauce, eggs, and vanilla extract.
  4. Stir wet mixture into dry ingredients; mix just until combined (do not over mix). 
  5. Stir in the chocolate chips.
  6. Spoon the batter into the prepared muffin tins until each one is almost full. 
  7. Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 18-20 minutes. To check for doneness, insert a tooth pick and if it comes out clean then muffins are done. (Freezing instructions begin here.)
  8. Let cool on a cooling rack for 10 minutes in the tin. Remove muffins and place on the cooling rack a bit longer.

Freeze For Later: Bake muffins as directed in recipe. Let cool completely. Then place in a gallon-sized freezer bag or container, seal tightly, and store for up to 3 months. 

Prepare From Frozen: Thaw muffins in the refrigerator or warm in the microwave.


Notes

Dairy-Free Version: Omit the chocolate chips or use a dairy-free brand like Enjoy Life Chocolate Chips.

Gluten-Free Version: Use this gluten-free Pumpkin Muffin recipe instead. It’s very similar and uses coconut flour instead of wheat flour.

Pumpkin Alternative: You could use butternut squash puree instead of pumpkin. Here’s how to make your own.

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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22 replies
  1. Morgan says:

    My notoriously picky five year old just came running into the kitchen asking what he was smelling coming from the oven. This is quick, easy, and delicious!

    Reply
  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!

    Reply
    • 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.

      Reply
  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?

    Reply
    • 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.

      Reply