Gluten Free Mini Chocolate Chip Muffins
These mini chocolate chip muffins are the perfect one bite snack recipe! They’re made in one bowl with simple pantry staple ingredients. They’re gluten free and can easily be made dairy free!

I’m kind of obsessed with anything in mini form. I’m also obsessed with muffins so these mini chocolate chip muffins are truly the perfect recipe. I always had some Entenmenn’s Little Bites muffins (or Little Debbie) in my lunch box at school, so this recipe gives me all the nostalgic feels.
Of course, this is a gluten free spin on the childhood classic, and can also be made dairy free and refined sugar free. The batter is made in just one bowl and takes all of 5 minutes to whip up.
They’re the perfect snack for kids and adults and can be made with chocolate chips or blueberries. The bake time is under 15 minutes, so they’re great when you need something to eat ASAP! If you love this recipe, try my peanut butter oat flour muffins or brownie bites next!
Why you’ll love this recipe
- Easy to make- one bowl!
- Dairy free friendly
- Soft & fluffy
- Perfect for an on the go snack

How to make mini muffins
MIX WET. Whisk together all wet ingredients until smooth. It helps to use all room temperature ingredients so the melted butter doesn’t harden when it comes into contact with the egg and yogurt.
WHISK DRY. Add in the dry ingredients, aside from the chocolate chips, until a smooth batter forms. Be sure to spoon and level the flour, don’t scoop right from the bag. Fold in the chocolate chips. Preheat the oven to 375 Fahrenheit.
REST BATTER. While the oven is preheating, let the batter rest for about 15 minutes. This will help them rise a bit more when baking.
BAKE. When the oven is ready, scoop the muffins into a 24 cavity lined mini muffin tin. Top with additional chocolate chips. Bake for 11-15 minutes or until a toothpick comes out clean. Let cool for 5-10 minutes, then remove from the tray and enjoy! Try my mini banana muffins next!

Ingredients & substitutions
FLOUR. I used gluten free all purpose flour to keep these mini muffins gluten free, but regular all purpose will also work if you are not GF. I do not recommend other types of flour such as almond, oat or coconut.
WANT TO SAVE THIS RECIPE?
If you use a different gluten free flour blend other than Bob’s Red Mill, make sure it has xanthan gum in the mix.
GREEK YOGURT. The yogurt in this recipe helps to keep the muffins moist. You can sub for sour cream and use dairy free or regular yogurt.
I don’t recommend regular yogurt (non-Greek) as it is more thin and liquidy and will change the texture of the muffins.
SUGAR. I used light brown sugar to give these a richer flavor, but any kind of sugar will work. You can use coconut sugar to make them refined sugar free, but keep in mind the color will be darker than pictured.
CHOCOLATE CHIPS. I recommend mini chocolate chips, but whatever you have will be fine. I like semi-sweet for the best flavor!

How to store and freeze
Once prepared, these mini chocolate chip muffins will keep for about 3 days in a container kept at room temperature or up to 5 days in the fridge. You can reheat them in the microwave to help the chocolate melt again.
I have not tried this myself, but you should be able to freeze just fine! Let them cool completely, then transfer to a freezer safe bag and freeze for 1-2 months. Let them thaw or reheat in the oven until warm through the center.
Sub with blueberries!
If you aren’t feeling the chocolate chips, I suggest wild blueberries since they are smaller and work better with mini muffins!

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Mini Chocolate Chip Muffins
by: claire cary
Ingredients
Wet
- 1 egg room temperature
- ½ cup light brown sugar
- 6 tablespoons butter melted
- 6 tablespoons room temperature greek yogurt
- 2 teaspoons vanilla extract
Dry
- 1 cup gluten free all purpose baking flour
- 1 ½ teaspoons baking powder
- ¼ teaspoon salt
- optional: 1/4 teaspoon cinnamon
- ¾ cup mini chocolate chips
Instructions
- Whisk together all wet ingredients until smooth.
- Whisk in the dry ingredients, aside from the chocolate chips, until a smooth batter forms. Be sure to spoon and level the flour, don’t scoop right from the bag.
- Fold in the chocolate chips.
- Preheat the oven to 375 Fahrenheit.
- While the oven is preheating, let the batter rest for about 15 minutes. This will help them rise a bit more when baking.
- When the oven is ready, scoop the muffins into a 24 cavity lined mini muffin tin. Top with additional chocolate chips.
- Bake for 11-15 minutes or until a toothpick comes out clean.
- Let cool for 5-10 minutes, then remove from the tray and enjoy!
Notes
Comments
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Super easy and very tasty as well! I used plant based butter and it worked fine. Do you think I could use sprinkles to make confetti mini muffins?
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Yes, should be fine!
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Is there a way to add protein powder to these and if so how much would be healthy without effecting the taste or texture negatively?
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You can try swapping about 2-3 tablespoons of flour for 2-3 tablespoons of protein powder.
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Okay thank you!
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These came out great! I made them for a youth group event and they were devoured lol, only thing I’d say though this was probably on me, but one of the 2 batches I made (I did one blueberry and one chocolate chip) I kinda ran out of a batter towards the end and I kinda had to stretch it, but my ratios were a bit off in terms of evening out each of the muffins. Still, these turned out very good ๐
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Can I use Greek vanilla yogurt?
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That’ll work!
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We have an egg allergy, what could I use instead of egg?
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You can try a store bought egg replacer like Bob’s Red Mill or a scant 1/4 cup of apple sauce.
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please let me know how to prepare gluten free flour. Many thanks in advance.
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Just buy in the store! I like Bob’s Red Mill 1:1 Baking Flour.
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Would almond flour work?
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No, generally, almond flour is not a safe sub for all purpose flour.
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