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Pumpkin Chocolate Chip Mini Muffins {Gluten-free, Dairy-free}

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Switch up the usual snacks and lunchbox treats with these gluten-free pumpkin chocolate chip mini muffins that are dairy-free, soy-free and nut-free too!

Gluten-free Dairy-free Pumpkin Chocolate Chip Mini-Muffins. Nut-free too!

My kids are crazy about muffins. I make muffins every few weeks and put them in the freezer. I love how easy it is to freeze muffins and then pull them out as needed for breakfast or for packing in their lunches.

I wanted to switch things up from the usual and get my kids to try something new. My family already loves gluten-free pumpkin bars, and gluten-free pumpkin cookies,  so I figured it was time to make a gluten-free pumpkin muffin!

Gluten-free Dairy-free Pumpkin Chocolate Mini-Muffins recipe. Nut-free too!

What could be better than adding chocolate chips to these muffins? Enjoy Life Foods sent me their new mini packs of semi-sweet chocolate chips this week to use in my sponsored post, so I used them in these mini muffins!

I’m super excited about these new Enjoy Life Foods Snack Packs of semi-sweet chocolate mini-chips! The gals from Enjoy Life Foods have been handing these out at Gluten-free Expos for a while, and everyone I know was giving them feedback to make this a product we can all buy. I think they’re perfect for travel, as I like to mix them in little packet of peanut butter, almond butter or Sunbutter to enjoy with pretzels for a snack. Also, when you’ve been stuck in the car all day long on a road trip, throwing one of these to each person in the car is a great way to sweeten everyone up!

I filled up a teal pumpkin with the new mini-chips snack packs and the new dark chocolate morsels snack packs and some non-food treats. I’ll have this by my front door on Halloween to give allergy-friendly treats and non-food treats to kids that have celiac or food allergies. If you aren’t familiar with the Teal Pumpkin Project, make sure you check it out too!

Allergy friendly Pumpkin Mini-Muffins Gluten-free, dairy-free, soy-free, nut-free recipe. They're delicious!

Notes on ingredients:

  • Use your go-to gluten-free all-purpose flour blend that fits with your allergies. If your blend contains xanthan or guar gum already, then you don’t need to add the xanthan called for in the recipe.
  • The semi-sweet chocolate mini chip snack packs are only available online from Enjoy Life Foods right now. But they’ll be in stores and on Amazon soon. In the meantime, if you are wanting to make these, just grab a big bag of Enjoy Life  semi-sweet chocolate mini chips from your local store or Amazon and use those.
  • As written, these are free of most of the top allergens. The only one I couldn’t eliminate just yet was egg. I tried to make this without the egg and with a popular egg substitution (applesauce) to big failures. If you do have an egg allergy in your home, feel free to try these with your favorite substitution.

Allergy Friendly Pumpkin Chocolate Chip Mini-Muffins. Recipe free of gluten, dairy, soy, corn, and nuts!

I adapted these amazing looking Pumpkin Cranberry Dark Chocolate Muffins from my friend Maegan (aka the Baker Mama). Her recipe was a great base to work with!

If you have extra cans of pumpkin on hand, be sure to try this Paleo Pumpkin Butter, it’s gluten-free and top 8 free too! These healthy brownies with pumpkin caught my eye as another gluten-free and dairy-free treat! And you can’t go wrong with these gluten-free vegan pumpkin chocolate chip cookies from my friend Chrystal either!

Make sure you try my gluten-free pumpkin bread recipe too!

If you make these and love them, please come back and give this recipe a 5 star rating in the recipe card! Feel free to comment with tips or to share any successful substitutions you made.

Yield: 48 mini muffins

Gluten-free Pumpkin Chocolate Chip Mini Muffins {Dairy-free}

Gluten-free Dairy-free Pumpkin Chocolate Chip Mini-Muffins. Nut-free too!

Switch up the usual snacks and lunches with these gluten-free pumpkin chocolate chip mini muffins that are dairy-free, soy-free and nut-free too!

Prep Time 20 minutes
Cook Time 11 minutes
Total Time 31 minutes


  • 2 cups good quality gluten-free flour blend
  • 1/2 tsp. xanthan gum (omit if your flour blend has xanthan or guar)
  • 2 tsp. baking powder
  • 1 1/2 tsp. cinnamon
  • 1 tsp. salt
  • 1/2 tsp. baking soda
  • 1 cup pumpkin puree (canned pumpkin)
  • 2/3 cup light brown sugar
  • 1/2 cup oil (your choice, depending on allergies)
  • 1/3 cup sugar
  • 1/4 cup applesauce
  • 2 eggs
  • 1 tsp. pure vanilla extract
  • 6 oz. Enjoy Life Foods semi-sweet chocolate mini chips (6- 1oz. pkgs or 1 cup from a large bag)


  • 4 oz. Enjoy Life Foods semi-sweet chocolate mini chips (4- 1oz. pkgs or rest of the large bag)


  1. Preheat oven to 375°. Spray mini-muffin pan well with cooking spray. Set aside.
  2. In a large bowl, whisk together flour, xanthan gum, baking powder, cinnamon, salt, and baking soda.
  3. In another large bowl, whisk together pumpkin puree, brown sugar, oil, sugar, applesauce, eggs and vanilla extract until smooth.
  4. Using a spatula, stir †he wet ingredient mixture into the dry ingredients until just combined. Stir in 1 cup (6 ounces) of semi-sweet chocolate mini chips.
  5. Use a small cookie scoop or spoon to fill mini muffin pan cavities almost completely full. Sprinkle the tops of all muffins with remaining chocolate chips.
  6. Bake for 11 minutes at 375°. Let muffins sit in the pan 5 minutes before carefully removing to a wire rack to cool.
  7. If you want to freeze these, let them cool completely, then place in a Ziploc Freezer Bag, remove excess air, label and freeze!
  8. Makes approximately 48 mini muffins.


You can make these as full-sized muffins if you prefer. Baking time will likely be just a few minutes more. Test for doneness with a toothpick - it should have moist crumbs but not wet batter.

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Gluten-free Dairy-free Pumpkin Muffins with Chocolate Chips. Easy, freezer friendly recipe that's nut-free too!

Looking for more uses for these handy Enjoy Life Foods snack packs of semi-sweet chocolate mini chips? Check out these recipes from my friends:

Gluten-free Espresso Brownie Bites 

Vegan Pumpkin Pudding 

Gluten-free Chocolate Cupcakes for Two

This sponsored post was created through my partnership with Enjoy Life Foods. As always, all opinions are my own. Collaborating with brands I love allows me to keep bringing you new and varied recipes! Thanks for your support!

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20 Best Gluten-Free Pumpkin Recipes

Thursday 14th of October 2021

[…] Pumpkin Chocolate Chip Mini Muffins by My Gluten-Free Kitchen […]


Friday 6th of November 2020

I just found your recipe and it's perfect!!! Do you have any ideas/recommends for using the recipe to make mini bread loaves?

Michelle Palin ~ My Gluten-free Kitchen

Tuesday 10th of November 2020

You could definitely do mini bread loaves. Fill the pans about 1/2 to 2/3 full. And then you'll just have to check them often. Start with 15 minutes and then go from there with adding additional time until they're done. Use the toothpick test. Let me know!


Sunday 21st of October 2018

I just finished baking these. They are so good. They do not look as pretty as yours. I had a hard time filling the muffin pan. The batter was very sticky.


Saturday 20th of October 2018

Just pulled these out of the oven and they are delicious! (I'm not even GF!) I made them for my husbands grandmother and I think they will be fall staple for family events! I hope they last until tomorrow! I followed the directions to a T and used Coconut oil and Cup4Cup GF flour from Target.

Heidi Wolff

Wednesday 10th of October 2018

These muffins were so good I had to make a second batch. They do not need the mini chocolate chips on top, they have enough in the batter. I didn't tell people these were gluten and dairy free and you couldn't tell. So easy my 4 year old granddaughter was able to help with most of the mixing.

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