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Gluten Free Pumpkin Chocolate Chip Muffins

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Gluten Free Pumpkin Chocolate Chip Muffins – These fluffy gluten free pumpkin muffins are our family favorite! The perfect yummy treat!

Gluten Free Pumpkin Chocolate Chip Muffin on a plate with a striped napkin.

Confession: we eat these muffins all year round.

Like, ALL year round.

They’re Milo’s favorite recipe of all time.

But, since the rest of the world follows pumpkin season, I thought it best to save this recipe for sharing until the fall. They’re just as great on a September morning before school as they are for an October breakfast-for-dinner or make-ahead breakfast on Thanksgiving morning. They’re exactly what fall should taste like. Fall is finally on the way and so are these amazing gluten-free (or not!) pumpkin chocolate chip muffins. Let’s jump in!

Basket of Gluten Free Pumpkin Chocolate Chip Muffins

What Makes These Pumpkin Chocolate Chip Muffins Amazing:

THEY’RE NATURALLY SWEETENED. I use pure maple syrup for these muffins. They’re just the right amount of sweetness for my taste, and leave plenty of room for the chocolate chips (which are definitely not naturally sweetened).

NO LEFTOVER PUMPKIN! I played with the amounts in the recipe to use exactly a full (15oz) can of pumpkin puree. I love when that happens. No leftovers to think about!

THEY CAN EASILY BE GLUTEN-FREE OR NOT. I use a one-to-one gluten free baking flour blend that’s a cup-for-cup substitute for white flour. If you’re not gluten free, you can easily swap in white flour (or half white and half whole wheat) for the gluten free flour blend. I used to do this all the time before I converted the recipe.

THEY CAN BE MADE MINI OR REGULAR SIZE. We really do eat these all year round, so sometimes I make mini muffins to pack in school lunches, and sometimes we make big ones to enjoy. It all works. (See below for my favorite muffin pans!)

Cooling Rack with Gluten Free Pumpkin Chocolate Chip MuffinsHand reaching for Gluten Free Pumpkin Chocolate Chip Muffin on a plate


LET’S TALK LEFTOVERS. These are divine fresh from the oven, but the recipe does make quite a few, so you’re bound to have leftovers unless you’re serving them to a large group. They freeze like a dream and we regularly thaw them to pair with lunch or snacks throughout the week. Just put them in a freezer-safe bag in the freezer and you can pull one out whenever the mood strikes!

MY FAVORITE MUFFIN PANS. If you’ve been here for a minute, you know I LOVE my silicone nonstick muffin pans. After the first 1 or 2 uses, they develop a truly nonstick coating (kind of like cast iron does) that means you don’t need muffin liners or nonstick spray. You can just pop the cooked muffins right out! Plus, they’re even dishwasher safe. Less waste + less fuss = more happiness! We have them in both standard size and mini muffin size and use both. (Note: we put the silicone muffin pan on a baking sheet for stability, as you can see in the video.)

GLUTEN-FREE FLOUR OR NOT! As I mentioned earlier, these are easily gluten free or not. I’ve had many friends make them with white flour over the years with great results. For gluten free flour, our favorite is Bob’s Red Mill one to one baking flour blend, but you can swap in Cup4Cup or King Arthur Flour’s 1 to 1 mix if you prefer.


Split open gluten free pumpkin chocolate chip muffin on a plate

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Gluten Free Pumpkin Chocolate Chip Muffin on a plate with a striped napkin.

Gluten Free Pumpkin Chocolate Chip Muffins

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5 from 1 review

  • Author: One Lovely Life
  • Total Time: 45 minutes
  • Yield: About 2 dozen standard muffins or 4-5 dozen mini muffins 1x


We love these with Enjoy Life brand chocolate chips, but you can also roughly chop your favorite dairy free chocolate bar to use instead, if you like. 


  • 1 (15oz) can pumpkin puree (NOT pie filling)
  • 1 cup orange juice
  • 1 cup gluten free oats (I use rolled, but quick-cooking will work too)
  • 1/2 cup pure maple syrup
  • 3 eggs
  • 3 Tbsp coconut oil, melted
  • 2 tsp cinnamon
  • 1 tsp ginger
  • 1/2 tsp cloves
  • 350g (about 2 1/2c) gluten free all purpose flour blend (We like Bob’s Red Mill 1:1 Gluten Free Baking Blend)*
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1 tsp salt
  • 1 cup (more or less, to taste) dairy free semi-sweet chocolate chips, such as Enjoy Life brand


  1. Whisk together pumpkin, orange juice, oats, syrup, eggs, coconut oil, cinnamon, ginger, and cloves. Stir in flour, baking powder, and baking soda. Fold in chocolate chips.
  2. Scoop by heaped tablespoons (I use a tiny cookie scoop) into a greased mini muffin pan. Bake at 375 degrees for 16-20 minutes, or until set. Allow to cool slightly, then remove from the pan and transfer to a cooling rack.
  3. Repeat with remaining batter until all muffins are baked. You should get about 5 dozen mini muffins (a few more or less perhaps).
  4. If using a standard muffin pan, fill muffin cups 3/4 full. Bake at 375 degrees for 20-25 minutes, or till set. You’ll get about 2 1/2 dozen muffins.
  • Prep Time: 10 minutes
  • Cook Time: 35 minutes
  • Category: Muffins, Breakfast
  • Method: Baking, Oven
  • Cuisine: American

Originally posted Sept 2014. Post, recipe & photos updated Sept. 2018.


  1. These are a family favorite! I’ve only made the original version, but I’ve tasted this one and loved it equally as well! They also passed the truest pumpkin loving man alive. These are delicious!

  2. Pesky pumpkin leftovers? No way! Put leftover pumpkin in an ice cube tray and freeze for pumpkin oatmeal! One cube of pumpkin in a standard size serving of oats (1/2 half cup oats/1 cup water) with walnuts, cinnamon, nutmeg and colves…to die for!!

    1. Krystal – You can use white flour (white flour made from wheat, not whole wheat flour) in exactly the same amount. Hope that helps!

  3. These muffins were delicious!!! I used all whole wheat pastry flour instead of gluten-free flour and used a neat egg replacer for the eggs (we have an egg allergy in our house). They are so delicious and my kids are obsessed with them!

      1. Hi Heather! We’ve used Neat brand egg replacer (the same as K did) before, and it works well! (It’s a powdered egg substitute)

  4. I am short one ingredient – OJ – to make these. How crucial is that ingredient? I really want to make these but this Snholding me back…ah!

    1. I haven’t tried substituting it out, so I can’t guarantee results, but you’d be welcome to try subbing something! Orange juice gives some of the acidity that reacts with baking soda to make nice, fluffy muffins. It doesn’t add much flavor-wise, but if you substitute it for another liquid, you’d probably want to make sure there’s some acidity there for best results. Some people have tried apple juice, or you could do milk + 1/2 tsp vinegar or so (for a buttermilk effect).

  5. I’ve made these twice and they are great! It would be nice to have another measurement for the pumpkin. I only had a larger 19oz can, so I had to get out the scale and weigh out 15oz, and even then I wasn’t sure if that was the right amount.

    Also, I didn’t have enough maple syrup this time so I substituted the same amount of brown sugar and it worked fine.

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