A good chocolate chip muffin should feel like a treat from the first bite. It should be soft, sweet, and full of chocolate, with a tender crumb that does not feel dry, gritty, or heavy. These gluten-free chocolate chip muffins are made for exactly that kind of muffin craving.

They are simple enough for breakfast but sweet enough to enjoy as an afternoon snack or lunchbox treat. The chocolate chips give them that classic bakery-style feel, while the soft muffin base keeps them from tasting like a plain muffin with chocolate tossed in as an afterthought.

This recipe, as written, also uses dairy-free ingredients, making it a helpful option when you need a gluten-free muffin that your friends who are following a dairy-free diet will also love. Make a batch for brunch, freeze some for later, or keep them on hand for an easy homemade snack.

Why These Are the Best Gluten-Free Chocolate Chip Muffins

These muffins use a mix of gluten-free flour and almond flour to create a softer, richer texture. The gluten-free flour blend gives the muffins structure, while the almond flour adds moisture and tenderness. Together, they help keep the muffins from turning out dry or crumbly.

The reverse creaming method also helps improve the texture. Instead of mixing the butter into the wet ingredients first, it gets worked into the dry ingredients. This coats the flour mixture and helps create a finer, more even crumb once the wet ingredients are added.

The batter also rests before baking, which gives the gluten-free flours time to hydrate. That short rest makes a big difference in the final muffin texture, helping the muffins bake up softer, fuller, and less gritty. Filling the muffin cups generously also helps create those tall, satisfying muffin tops.

What You’ll Need for Gluten-Free Chocolate Chip Muffins

I like to get everything out before I start making muffins for two reasons. First, I can make sure I have all the ingredients I’ll need before I start. That way, I won’t have to run to the grocery store or dig out a make-do replacement ingredient in the middle of making these muffins.

Second, getting everything out first gives me a chance to bring some of the ingredients up to room temperature. Room-temperature ingredients are usually easier to mix into the muffin batter.

Equipment

• Digital Food Scale
• Stand Mixer with Paddle Attachment
• Small Mixing Bowl
• Rubber Spatula
• Two Muffin Tins
• Measuring Cups and Spoons
• Toothpicks
• Wire Cooling Rack

Ingredients

I’ll usually like to make sure I have enough of these before I start. (I have come close to running out of xanthan gum before.)

• Gluten-Free Flour Mix
• Almond Flour
• Brown Sugar
• Baking Powder
• Baking Soda
• Xanthan Gum
• Salt
• Dairy-Free Butter
• Almond Milk
• Sour Cream
• Large Eggs
• Pure Vanilla Extract
• Apple Cider Vinegar
• Dairy-Free Chocolate Chips or Chocolate Chunks

Key Ingredient Roles

Ever gotten curious about how gluten-free baking even works? Each of these ingredients brings something to the recipe that makes it possible. Here’s a quick rundown.

Gluten-Free Flour Mix

280 grams (about 2 1/2 cups) gluten-free flour mix

Buying a gluten-free flour mix in the store can be tricky, especially if you don’t need a mix that doesn’t contain xanthan gum. (We’ll add that separately with this recipe.) So I’ll use this recipe to make my own gluten-free flour mix to get nearly everything I need to replace the gluten. It’s a mix of white rice flour, brown rice flour, tapioca powder, cornstarch, and potato flour.

Almond Flour

80 grams (about 3/4 cups) almond flour

The thing to remember about almond flour is that (obviously) it’s made from almonds, so it is usually higher in fat than other types of flour (50.2 grams of fat per 100 grams of flour, according to USDA FoodData Central). However, its protein and fiber content are roughly comparable to chickpea flour, and I can usually find almond flour even in stores that don’t stock chickpea flour, which is what we want. The protein and fiber form a network that supports the muffins’ structure and holds in moisture.

Brown Sugar

150 grams (about 2/3 cups) brown sugar

Normally, I’d go with granulated sugar with muffins, but I tried it once with brown sugar because I was out of granulated sugar and ended up liking it a little bit better. Brown sugar contains a bit of molasses, which I think gives baked goods a slightly more sophisticated flavor. (Naturally, kids barely notice the difference if you don’t tell them. They just know that they like chocolate chip muffins.)

Baking Powder

2 teaspoons baking powder

Baking powder is one of the two chemical leavening agents we’ll use for these muffins. Baking powder already contains everything it needs to add the carbon dioxide bubbles that give baked goods a lighter, fluffier texture.

Baking Soda

1/2 teaspoon baking soda

Baking soda is a bicarbonate that reacts with the acids in other ingredients to create more air bubbles and fluff these muffins up.

Xanthan Gum

1/2 teaspoon xanthan gum

Xanthan gum is a common gluten replacement in gluten-free recipes. It supports structure and elasticity, which is important for proper texture in these muffins. It also serves as a binding agent that helps keep the muffins from falling apart after you take them out of the oven.

Salt

1/4 teaspoon salt

Salt provides a complement for the sweet flavors in these muffins without overwhelming it with saltiness.

Dairy-Free Butter

9 tablespoons (a little more than 1/2 cup) butter

Softened dairy-free butter provides a little extra richness without overloading the muffins with unhealthy fat. Sticks of Country Crock plant-based butter are my favorite because they have heart-healthy monounsaturated fat and are easy to work with.

Almond Milk

4.5 ounces (about 2/3 cup) almond milk

Almond milk adds moisture and a little extra richness to the muffins. It will add a mild nutty flavor, too.

Dairy-Free Sour Cream

140 grams (about 2/3 cups) dairy-free sour cream

Sour cream adds a richer flavor and more moisture, which helps give the muffins a tender crumb.

Large Eggs

2 large eggs

When mixed with other ingredients, the proteins in eggs uncoil and form a network that holds in moisture and provides most of the binding power that holds the other ingredients together.

Pure Vanilla Extract

1 1/2 teaspoon vanilla extract

Vanilla extract adds a creamy sweetness to these muffins. If you have to choose among types of vanilla extract, I recommend Madagascar vanilla extract because it delivers the sweet flavor you want, with floral and fruity notes.

Apple Cider Vinegar

1 teaspoon apple cider vinegar

Apple cider vinegar adds the acid that the baking soda needs to react with. It tends to have a stronger acidic flavor than white vinegar, so be careful not to add too much.

Dairy-Free Chocolate Chips or Chocolate Chunks

1 cup chocolate chips or chocolate chunks, plus more to add to the top of the muffins

Chocolate chips or chunks add the sweet chocolate flavor that everybody loves. I like to use the Enjoy Life brand for dairy-free, semi-sweet chocolate chunks.

Method for Making Gluten-Free Chocolate Chip Muffins

Let’s jump right into making these muffins. The hard part’s usually being patient as they rest and then bake!

Step One: Mix Dry Ingredients

Add the gluten-free flour mix, almond flour, brown sugar, baking powder, baking soda, xanthan gum, and salt to the bowl of the stand mixer. Mix with the paddle attachment for 30 seconds until combined.

Step Two: Add Butter

Add the softened butter and mix for 45 seconds, occasionally scraping down the sides of the bowl, until the mixture looks crumbly.

Step Three: Mix Remaining Wet Ingredients in Small Bowl

In a small bowl or measuring cup, stir together the almond milk, sour cream, eggs, vanilla extract, and apple cider vinegar until evenly combined.

Step Four: Gradually Add Wet Ingredient Mix to Dry Ingredients

With the mixer on low, slowly add the wet ingredient mixture to the dry ingredients until lightly combined

Step Five: Finish Mixing Ingredients Together

Scrape down the bowl and turn the speed up to medium. Mix for 2 minutes.

Step Six: Fold In Chocolate Chips or Chunks

Lightly fold in the chocolate chips or chunks until evenly distributed through the batter.

Step Seven: Let Batter Rest

Set batter aside to rest for 30 minutes. This lets the flour absorb moisture more completely, so the muffins don’t dry out too much during baking. The baking powder and baking soda can also begin forming the carbon dioxide bubbles that give the muffins a fluffier texture.

Step Eight: Preheat Oven and Prepare Muffin Tins

While the batter is resting, preheat your oven to 375 degrees Fahrenheit (190 degrees Celsius). Spray the insides of all 12 cups of one muffin tin and 3 cups of a second muffin tin with cooking spray.

Step Nine: Portion Muffin Batter to Prepared Muffin Tins

When the muffin batter has finished resting, begin portioning it into the 15 prepared muffin cups. The muffin batter should be roughly evenly distributed between the cups. Lightly sprinkle extra chocolate chips over the top of the muffins, lightly pressing them into the batter.

Step Ten: Bake Muffins

Bake muffins for 20-22 minutes until a toothpick inserted into the center of a muffin comes out clean.

Step Eleven: Cool Muffins

Cool the muffins for about 10 minutes in the muffin tins, then transfer them to the cooling racks to finish cooling. This gives the muffin centers time to finish setting.

Step Twelve: Eat or Store Muffins

You can eat the muffins right away or store them in an airtight container on the kitchen counter for up to 3 days.

Substitutions for These Gluten-Free Chocolate Chip Muffins

Psyllium husk powder and ground chia seeds can replace the xanthan gum at a 1:1 ratio. For more information on xanthan gum replacements, feel free to check out our 10 Best Xanthan Gum Replacements.

For each egg you would like to replace, mix one tablespoon of ground chia seeds or flaxseed meal with three tablespoons of water. Let the mixture sit for a few minutes until it forms a gel.

Dairy-based milk, butter, and sour cream can replace the dairy-free options if you don’t mind that this recipe won’t be dairy-free.

For a little variety, stir 1/2 cup chopped pecans into the batter with the chocolate chips.

Troubleshooting Guide for Gluten-Free Chocolate Chip Muffins

I think these muffins are pretty easy to make, but I can understand if they don’t turn out perfectly the first time! Here’s a troubleshooting chart for common issues with these muffins.

Problem	Likely Cause	How to Fix It
Muffins are dense or heavy	The batter was undermixed after adding the wet ingredients, or the ingredients were too cold	Use room-temperature ingredients and mix for the full 2 minutes after scraping down the bowl. The batter should look pale and fluffy before the chocolate chips are folded in.
Muffins are gummy in the center	They were underbaked, measured with too much liquid, or cooled too soon in a sealed container	Bake until a toothpick comes out clean or with a few moist crumbs, not wet batter. Let the muffins cool properly before storing.
Muffins did not rise well	The batter did not rest long enough, the muffin cups were underfilled, or the leavening was old	Let the batter rest for the full 30 minutes, fill the cups to the top, and check that the baking powder and baking soda are fresh.
Muffin tops are flat instead of domed	The batter was too loose, the oven was not hot enough, or the cups were not filled high enough	Preheat the oven fully to 375°F and portion the batter all the way to the top of each muffin cup. Avoid adding extra milk or sour cream.
Muffins are dry or crumbly	Too much flour was added, the muffins were overbaked, or a different flour blend absorbed more moisture	Weigh the flour instead of scooping by volume. Start checking at the lower end of the bake time and avoid swapping flour blends unless you know they behave similarly.
Muffins fall apart when removed from the pan	They were removed too soon, the pan was not sprayed well, or the muffins were slightly underbaked	Let them cool in the pan for 10 minutes before removing. Spray each muffin cup thoroughly, not just the top of the pan.
Muffins stick to the pan	The muffin cups were not greased well enough	Coat each cup with cooking spray before adding batter. For easier cleanup, use parchment-style liners and spray those lightly too.
Muffins have greasy bottoms	The dairy-free butter was too soft or melted, or the batter was overworked after the butter was added	Use softened butter, not melted butter. After adding it to the dry ingredients, mix only until the mixture looks evenly crumbly.
Chocolate chips sink to the bottom	The batter was too thin, the chips were too large or heavy, or the batter was not rested	Rest the batter before baking so the gluten-free flours can hydrate. Use regular or mini chocolate chips if large chunks keep sinking.
Muffins have tunnels or large holes inside	The batter was mixed too aggressively after the wet ingredients were added, or air pockets formed while portioning	Mix as directed, then fold in the chocolate gently. After scooping the batter into the pan, lightly tap the pan once or twice to settle the batter.
Muffins brown too quickly	The oven runs hot, the pan is dark metal, or the muffins were baked too high in the oven	Bake on the center rack. If your oven runs hot, check early or reduce the temperature slightly next time.
Muffins are pale on top	The oven was not fully preheated, the pan was overcrowded, or the muffins needed another minute or two	Preheat the oven completely before baking. Bake until the tops are set and lightly golden.
Muffins taste bitter or metallic	Too much baking powder or baking soda was added, or the leavening was not evenly mixed	Measure leaveners carefully and mix the dry ingredients well before adding the butter. This helps distribute the baking powder, baking soda, salt, and xanthan gum evenly.
Muffins taste bland	The salt was left out, the chocolate was too mild, or the vanilla was undermeasured	Do not skip the salt or vanilla. Use good semi-sweet dairy-free chocolate chips or chunks for the best flavor.
Muffins seem too moist after storage	They were stored before cooling completely, which trapped steam	Cool the muffins completely before sealing them in a bag or container. If they soften after storage, warm them briefly before serving.

FAQ for Gluten-Free Chocolate Chip Muffins

Do you have any questions about these gluten-free chocolate chip muffins? I did my best to answer some of the most commonly asked questions here. If you think of one we haven’t answered yet, feel free to ask in the comments section, and we’ll answer as soon as possible.

Can I make mini muffins?

I’ve done that before! Just use a couple of mini muffin tins. The baking time will be shorter, so you’ll have to start checking them sooner.

I would like jumbo muffins like the ones at Sam’s Club. Is there a muffin tin with cups big enough?

I found a jumbo muffin tin on Amazon that should work! You will likely have to adjust the baking time to suit, and not getting the top too brown will be the tricky part.

Can I freeze them?

They can be frozen if you place them in a freezer-safe resealable bag or an airtight container. Thaw them out on the counter overnight before using.

I have a friend whose digestive system reacted badly to Xanthan gum. Can I leave it out?

It happens! Xanthan gum is a common replacement for the gluten in wheat flour. However, you can replace it with an alternative, such as psyllium husk powder or ground chia seeds, if you have to.

Somebody wouldn’t believe me when I said they weren’t raisins. How can I convince them?

Well, you may have somehow gotten a reputation as a prankster if they won’t believe you. The easiest way to avoid this is to use chocolate chips rather than raisins whenever you make these muffins. (Not that I have anything against raisin muffins, but I could see how such a “prank” could happen!)

More Gluten-Free Muffins

Did you like these muffins? Here’s more muffins to try next time you go on a baking spree!

• Almond Flour Blueberry Muffins
• Gluten-Free Oatmeal Apple Muffins
• Soft Gluten-Free Blackberry Muffins with Irresistible Crumb Topping
• Almond Flour Banana Muffins That Are Actually Fluffy
• Tender Lemon Chia Seed Muffins

Did you like these muffins? Be sure to let us know what you thought in the comments section, and don’t forget to rate this recipe!