Gluten Free Chocolate Muffins


If you like breakfast treats, you will love these gluten free chocolate muffins! They’re sweet, but not too sweet, moist, fluffy, full of rich chocolate flavor, and come together quickly for a stress-free weekend brunch. 

Gluten-Free Chocolate Muffins Recipe

I don’t know about you, but I’ve always loved a fruity muffin. Blueberry banana muffins were a staple at our house growing up. 

I think I was probably an adult before I every had a muffin with chocolate chips in it, and I was stunned. After all, is it still a muffin if it tastes like a dessert? 

The answer, of course, is yes. And while I definitely wouldn’t recommend starting your day with a dessert-type muffin every day, who doesn’t love the occasional treat? And let’s not forget that pancakes, waffles, and donuts are all considered totally acceptable breakfasts, so why not chocolate muffins? 

Pro-tip: Add some pecans or chopped walnuts to your muffin batter for some crunch!

You’re gonna love the chocolate on chocolate flavor of these gluten free chocolate muffins! 

Ingredients for gluten free chocolate muffins

mis en place for gluten-free chocolate muffins

This gluten free muffin recipe calls for just a few simple ingredients, so it’s easy to stir together any time you feel like baking 

You’ll need: 

  • Gluten free flour blend (more on that below)
  • Brown sugar
  • Cocoa
  • Baking soda, 
  • Salt
  • Oil (I use light olive oil. Melted coconut oil is also good)
  • Vanilla extract
  • Instant coffee (optional, but helps intensify the chocolate flavor)
  • Eggs
  • Milk
  • Chocolate chips

What is the gluten free flour mix made of? 

This is an important point in gluten free baking. In fact, if you’ve been at it for a while, you already know that not all flour blends are created equal. 

I’m personally a big fan of Judee’s gluten free flours, and mixing my own. For years, I used a homemade inexpensive gluten free flour mix using brown and white rice flours, and corn starch. If you’re looking to cut costs to the minimum, that flour mix will definitely do the job. 

In my mind, the flour blend not only needs to mimic the texture of wheat flour in the finished baked good, it also needs to have a balance of flavor. So, I like to use a bit of quinoa flour, or perhaps some ivory teff. White sorghum flour is also very good. And finally, superfine brown rice flour is another versatile favorite. 

In terms of starches, cornstarch and arrowroot powder both behave very similarly, and I rely on them the most. 

For this recipe, you’ll need 1 1/4 cups total of flour. So I used: 

With that said, if you’re using a commercial flour mix, I had very good success using Kind Arthur All Purpose gluten-free flour blend in this recipe.    

chocolate muffin on a plate with a bite out of it.

Substitutions and add-ins

When it comes to making muffins, you can be really flexible with add ins. Want to add some fruit? Go for it! Frozen or fresh? Doesn’t really matter as long as it’s not watery when you add it (i.e. some frozen fruit gets very water as it thaws, so it needs to still be frozen when you add it). 

Some fruits would be really tasty in chocolate muffins. Think chopped strawberries or cherries. 

But you also might want to add mini marshmallows and chopped almonds and call them rocky road muffins. 

Or perhaps you’ll want to add pecans or walnuts. The sky is pretty much the limit here!

How to make dairy free chocolate muffins

This is an easy ingredients substitution; just use almond milk. Be sure to also use dairy-free chocolate chips. 

Another awesome substitution would be white chocolate chips. 

For making more healthy chocolate muffins, you can substitute the sugar for turbinado, coconut sugar, or 3/4 cup of maple syrup.

How to make gluten-free chocolate muffins

Here are the easy-to-follow instructions for making homemade chocolate muffins that are completely gluten-free. You can print these instructions and the full list of ingredients and measurements out in the recipe card below.     


  1. First, Combine the flour, sugar, cocoa, baking soda, salt, and instant coffee together in a large bowl
  2. Create a well in the center or the dry ingredients and drop in the eggs
  3. Whisk the eggs, and add the oil and milk
  4. Stir into the flour mixture until just moistened
  1. Stir in chocolate chips and any other add ins you’re using
  2. Spoon batter batter between a dozen paper-lined muffin cups and bake at 350º for 18 minutes until done
  3. Remove from oven and let cool

FAQs and tips for making homemade gluten free chocolate muffins

This is such a simple recipe, it’s hard to go wrong, but I do have a few success tips and frequently asked questions to share with you. 

Do you need to use paper liners to make these chocolate muffins? 

No, You’re welcome to grease your muffin pan with butter, or give it a quick spritz of cooking stray. I typically prefer liners though, because it makes things super easy, and I virtually never have to give my pans more than a quick rinse before putting the away. 

How are chocolate muffins different from chocolate cupcakes? 

Good question! While these muffins are very dessert-like, they’re not cupcakes. They’re less sweet, denser, and have an irregular, domed top, not meant to be smooth for icing. I’m not saying you couldn’t ice them and serve them as dessert, because with a few tweaks – mostly omitting topping them off with extra chocolate chips – you totally could. But they’re not quite a cupcake. 

Can you add bananas to this muffin recipe? 

Depends. Stirring chopped bananas into the batter, yes. Mashing bananas to add to the batter, even if it’s to replace the oil, no. You’d be changing the texture and composition of the batter. We do have a delicious gluten free banana bread you can make though!

Can I add zucchini to the batter? 

No. Again, you’d be adding a lot of moisture, so I wouldn’t recommend it. I would, however, recommend our gluten free chocolate zucchini bread recipe. You could even make it in muffin pans instead of a loaf (reduce the cooking time to about 20 minutes).

Can I omit the chocolate chips?

Yep. You can leave them out, swap them with a different kind of chips (peanut butter would be amazing), or replace them with nuts. Dark chocolate chips are also legit.

chocolate muffin on a plate with chocolate chips and butter.

How to store gluten-free chocolate muffins

If you have leftover muffins, let them cool completely before storing them. Partly so moisture doesn’t condense inside our container, and partly because melty chocolate chips make a mess. 

  • After they’re cool, simply put them in an airtight container (rubbermaid, ziplock bag…) at room temperature on your kitchen counter for 1-2 days. 
  • You can also put leftover muffins in the freezer. To do this, I recommend placing them in a ziplock bag, or wrapping in plastic wrap, and them covering them with foil. 
  • To thaw, put them in your refrigerator overnight
  • To reheat, zap in the microwave (unwrapped) for 15-20 seconds, or place them (again, unwrapped) in a 350º oven for 10 minutes

More gluten free muffins to try: 


Gluten Free Chocolate Muffins

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  • Author: Elise New


  • 1 1/4 cups gluten free flour blend
  • 1 cup granulated sugar
  • 1/2 cup cocoa powder
  • 1 teaspoon instant coffee (optional, but adds to the richness of the chocolate flavor)
  • 3/4 teaspoon baking soda
  • 1/4 teaspoon salt
  • 2 eggs
  • 1/3 cup light tasting oil
  • 1 teaspoon vanilla extract
  • 3/4 cup milk
  • 1 1/4 cups chocolate chips


  1. Preheat oven to 350º
  2. In a large mixing bowl, combine flour, sugar, cocoa, instant coffee, baking soda, and salt
  3. Make a well in the center, and add the eggs. Whisk them quickly to break up the yolks and whites
  4. Add oil, vanilla, and milk
  5. Stir until just combined
  6. Stir in 1 cup of chocolate chips
  7. Divide batter between 12 paper-lined or greased muffin tins
  8. Top with remaining chocolate chips 
  9. Bake in preheated oven for 18-20 minutes until a toothpick inserted in the center comes out clean
  10. Remove from oven and let cool on a wire rack a few minutes (or completely) before serving
  11. Enjoy!

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  1. Got to the middle of the recipe and surprise! add a cup of chocolate chips… doesn’t totally ruin the recipe, but might be nice to add them to the ingredients list.

  2. Looked again and they’re there… must have been blocked by an ad- they can be so annoying and, even though I don’t think they’re designed to work that way, seem to be blocking a lot of content these days! It’s a yummy recipe and I’m glad you posted it…I hope no one else has my problem or at least reads my comment before they miss the extra chocolate hit in their muffins/ cupcakes… Thanks

  3. We reached the halfway point in the recipe, and lo and behold! Include a cup of chocolate chips… does not necessarily harm the dish, but could be a pleasant addition.

  4. The chocolate Muffin Recipe is amazing! And it is gluten-free..

    Elise is awesome…I look forward to trying some of her other gluten-free recipes.

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