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Gluten Free Chocolate Chip Pumpkin Muffin Recipe (Plus With-Gluten Alternative)

Updated on December 4, 2016

Pumpkin Paired with Chocolate for a Moist, Delicious Muffin

With so many tasty fall-inspired pumpkin baked goodies out there, the gluten-free person needs a tasty treat to nosh on too! You won't feel left out when you taste how moist, chocolatey and pumpkin-y (is that a word?) these muffins are. They're perfect with pumpkin flavored coffees, as breakfast muffins, an afternoon snack or for a fall-themed brunch.

Best of all, even non-GF (gluten-free) eaters will rave about them. I've served these muffins at a number of brunches and I get multitudes of comments on how good they are. You can even make them as mini-muffins if you so desire. Get the recipe and learn more about some of the health benefits in these yummy muffins.

These are my family's go-to muffins...hands-down our favorites ever. That's saying a lot since I bake quite a variety of muffins. I've tweaked this recipe over the years, so you'll benefit from the changes I've made to get it to its healthiest and most delicious.

For my gluten-eating friends out there, I also included a version with regular flour and some nutritious ingredient substitutions that don't compromise on flavor.


photo credit:

Pumpkin - A Nutritious Vegetable Hiding in a Muffin

This quintessential icon of fall has some great nutrients going for it. While a muffin by definition isn't necessarily 'healthy', the nutritional benefits pumpkin provides may help you justify eating these delicious muffins. ;)

Next time you dive into a slice of pumpkin pie, pumpkin muffin or dish up some pumpkin soup, remember that cooked pumpkin is a very good source of dietary fiber at 3 grams per serving. Add that to being a good source of Vitamin A, Vitamin C, Riboflavin, Potassium, Manganese and Copper and you've got yourself a superstar of a fall vegetable.

More pumpkin nutrition data

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How Do You Like Your Pumpkin?

What's your favorite way to enjoy pumpkin?

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Pamela's Gluten Free Ultimate Baking Mix - The mother of all gluten-free baking mixes

Pamela's Products Gluten Free Baking and Pancake Mix, 4-Pound Bags (Pack of 3)
Pamela's Products Gluten Free Baking and Pancake Mix, 4-Pound Bags (Pack of 3)

This baking mix is not only incredibly versatile in creating gluten free baked goods, but it's got amazingly great texture and taste. I've tried all sorts of GF baking mixes and flours, and none compare to Pamela's. It's a lot cheaper online per ounce than getting it in Whole Foods or other health food stores. I've made muffins (of course), cakes, coffee cakes, banana breads, cookies, etc. with this mix, and all have turned out so well that people who don't eat gluten-free have raved about them.


I adapted this recipe from the regular (with gluten) version on The flaxseed idea is mine; I think it's a great improvement on some already-yummy muffins. I also swapped out some greek yogurt for half of the oil, which gives the recipe more protein and makes the texture, well, a bit less oily.

I doubled the cinnamon and added pumpkin pie spice because the original recipe was a bit bland in my opinion. It's got a bit more pumpkin-y kick now.

Cook Time

Prep Time: 10 - 15 min.

Total Time: Approx. 30 min; give or take.

Serves: 24 - 30 muffins


  • 4 eggs
  • 2 cups sugar (I use natural cane sugar/sucanat to make this a bit healthier)
  • 1 - 16oz can of pureed pumpkin
  • 3/4 cup oil (I'm not kidding). Use olive oil for heart-healthier fats. You can try butter - but it's not as good. Trust me.
  • 2/3 cup plain or vanilla flavor greek yogurt
  • 3 cups Pamela's All Purpose Baking Mix (Pamela's yields the best results by far but you can substitute another gluten-free mix)
  • 1/8 tsp baking soda
  • 1/8 tsp baking powder
  • 2 tsp ground cinnamon
  • 2 tsp pumpkin pie spice
  • 1/4 cup flax seed meal (ground flax seeds)
  • 1 tsp salt
  • 3/4 package mini chocolate chips -- more or less to taste.


  1. In a large mixing bowl, beat eggs, sugar, pumpkin, oil and greek yogurt until smooth. Add in dry ingredients and mix well. Fold in chocolate chips. Fill greased or paper-lined muffin cups 3/4 full. Bake 16-20 minutes at 400 degrees.
  2. For mini-muffins, use a mini-muffin pan. Make sure not to overfill the cups; around 2/3 to 3/4 full is plenty. Cut the bake time in half; watch muffins carefully to make sure they don't burn.
  3. *********For NON-gluten free muffins, substitute regular flour for the gluten-free baking mix, and increase the baking soda and baking powder to 1 teaspoon each. ************

Freezer Friendly

These muffins take well to freezing. After cooling, put them in a plastic resealable bag, squeeze out all of the air, and store in the freezer. To thaw, just pop them in the microwave on defrost, and you get a quick muffin treat.

With-Gluten Recipe - Chocolate Chip Pumpkin Muffins

  • 4 eggs
  • 1 cup sugar (I use natural cane sugar/sucanat to make this a bit healthier)
  • 1 cup unsweetened applesauce
  • 1 - 16oz can of pureed pumpkin
  • 1/2 cup coconut oil (heated in microwave to make it fully liquid)
  • 1/4 cup olive or vegetable oil
  • 2/3 cup plain or vanilla flavor greek yogurt
  • 1/4 cup flax seed meal (ground flax seeds)
  • 1 cup coconut flour
  • 2 cups flour
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 2 tsp ground cinnamon
  • 2 tsp pumpkin pie spice
  • 1 tsp salt
  • 3/4 package mini chocolate chips -- more or less to taste.

In a large mixing bowl, beat eggs, sugar, applesauce, pumpkin, coconut oil, olive oil and flaxseed meal until smooth. In a separate bowl stir together dry ingredients (except for chocolate chips), then gradually add to the pumpkin mixture, stirring until just mixed. The batter will be pretty thick.

Stir in mini chocolate chips. Fill paper-lined muffin cups 3/4 full. Bake 16-20 minutes at 400 degrees. Makes approximately 30-35 standard size muffins. They aren't the prettiest, but they sure make up for it in flavor.

For mini-muffins, use a mini-muffin pan. Make sure not to overfill the cups; around 2/3 to 3/4 full is plenty. Cut the bake time in half; watch muffins carefully to make sure they don't burn.

3 stars from 7 ratings of Gluten Free Chocolate Chip Pumpkin Muffin Recipe

Tips for Making Your Muffins the Best They Can Be

These muffins do all right with greased muffin cups, but I've gotten better results using paper liners. Maybe you have a lot better muffin pans than I do, so use your own judgement.

If you're using a gluten-free baking mix other than Pamela's, check to see if it already contains baking powder or baking soda. If so, use the recipe as written. If not, increase baking powder and baking soda to 1/2 teaspoon each.

So What's the Deal with the Flaxseed in These Muffins?

Flaxseeds are small but mighty in terms of health. They contain Omega-3 fatty acids which are very heart-healthy, Lignans which have antioxidant qualities as well as both soluble and insoluble fiber. The flaxseed is necessary to the with-gluten recipe, since it balances out the moisture of the applesauce. For the the gluten-free the taste isn't altered much; flax just adds just a teeny hint of nuttiness that in my view accentuates the pumpkin.

Teff Flour Option

Want to pack an even bigger nutritious punch in your muffins? For every cup of baking mix, replace 1/4 cup of it with 1/4 cup of Teff flour. It's high in calcium, iron and protein, and has a great balance of amino acids. Teff is a tiny grain native to Ethiopia.

My Favorite Teff Flour

Bob's Red Mill Teff Flour, 24 Oz (4 Pack)
Bob's Red Mill Teff Flour, 24 Oz (4 Pack)

First of all, Bob's Red Mill brand is readily available in many health food stores and even some regular grocery stores. I actually found my first bag of it in the regular grocery in the health food section. I like how Bob's Red Mill puts good descriptions of the nutritional benefits of each product they produce right there on the bag, as well as recipe suggestions. I haven't made the recipe on the bag, but this teff does very well in my pumpkin muffins.


Your Thoughts on Pumpkin Muffins

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    • SusanAston profile image


      6 years ago

      I haven't eaten pumpkin pie for many years. The first time was on a holiday to Canada and it was so delicious

    • anamana profile image

      Molly Evans 

      6 years ago from Los Angeles

      These sound amazing! I once made pumpkin chocolate cookies that were off the charts delicious.

    • profile image


      6 years ago

      I like the recipe but I think I would like to try it with fresh pumpkin that I cook and blend in a blender in place of the canned pumpkin.

    • JessicaBreeze profile image


      6 years ago

      I will have to try this without the dairy otherwise it sounds yummy!

    • TreasuresBrenda profile image

      Treasures By Brenda 

      6 years ago from Canada

      Sounds like a good recipe. I like mufffins that are nutritious...rather than the cake-like ones available in the stores.

    • wheresthekarma profile image


      6 years ago

      Great lens, i referred to it on my gluten free blog!

    • profile image


      6 years ago

      This sounds quite tasty to me! Thanks for sharing!

    • Sylvestermouse profile image

      Cynthia Sylvestermouse 

      7 years ago from United States

      This recipe sounds delicious and definitely one I will try!

    • SquidooMBA profile image


      7 years ago

      My wife just made these and they were very tasty! Thanks for the recipe...

    • profile image


      7 years ago

      I will wait for my sister JBhumbug to cook them then try them lol! Great lens well thought out lots of info and well designed thanks.

    • jbhumbug profile image


      7 years ago

      Haven't tried as yet but look forward to making these thank you...just bought a rabbit and called it pumpkin lol

      glad you can can freeze them as well. i like to bulk cook :)

    • BunnyFabulous profile imageAUTHOR

      Erin Hardison 

      7 years ago from Memphis, TN

      @canoz: For a low glycemic index diet, replace the sugar with something like WheyLow sweetener:, or Truvia (a stevia sweetener) You should be able to order either on, or ask your local health food store.

    • profile image


      7 years ago

      These look delicious! Thanks for sharing your recipe!

    • canoz profile image

      Heather Bradford 

      7 years ago from Canada

      Thanks for the great recipe. Can't wait to try it. I have a low GI diet and am wondering if I should cut back the sugar at all? Are they very sweet?? I would also love to know how you added the printer version to your lens (how brilliant!!). Can you tell me how this is done or point me in the right direction to finding out? Thank you, thank you!!

    • retta719 profile image


      7 years ago from United States

      Yummy!!!! *~*~*~*~*~angel dust from the gluten free neighborhood angel~*~*~*~*~*

    • profile image


      7 years ago

      I'm not much of a baker. But I do enjoy pumpkin and both these recipes sound appealing to eat.

    • ElizabethSheppard profile image

      Elizabeth Sheppard 

      7 years ago from Bowling Green, Kentucky

      This sounds scrumptious.

    • annieangel1 profile image


      7 years ago from Yorkshire, England



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