These gluten free chocolate chip muffins have that moist and tender cake-like crumb everyone loves, and just enough chips to tempt your pickiest eater. They’re just right for breakfast, or an afternoon snack.

What makes this recipe for gluten free chocolate chip muffins special

These gluten free chocolate chip muffins, like all muffins, have a slightly denser texture than cake. But the crumb is so tender and moist, it leans a bit closer to cake-like than you might expect.

I do have a very adaptable recipe for gluten free muffins, and it’s a great recipe. But like an all purpose gluten free flour is good for all purposes, but not ideal for certain more nuanced applications, this muffin recipe is what my dream of a chocolate chip muffin looks like.

To me, a really special chocolate chip muffin has a slightly more tender crumb. So it starts with a slightly softer batter. Here, the flour blend favors starch a bit, for softness, and of course there’s the buttermilk.

But the combination of melted butter and a neutral oil really helps keep the muffins moist, and still flavorful. And never, ever oily-tasting.

Some notes on gluten free chocolate chip muffins ingredients

  • All purpose gluten free flour – You’ll need to use one of my recommended blends of an all purpose gluten free flour, and in this recipe I really recommend using Better Batter gluten free flour classic blend (or my mock Better Batter recipe), to get the same tender results that I do.
  • Cornstarch – If you’re using Better Batter’s classic blend like I usually do (mostly for ease, and reliability), you’ll need to add some cornstarch to help lighten the blend a bit and soften the relative consistency of the batter. If you’re using a higher starch blend, like Cup4Cup, replace the cornstarch with more Cup4Cup, by weight for the same results.
  • Baking powder – Baking powder gives rise to these muffins, so make sure yours is fresh or your muffins will be dense and gummy.
  • Baking soda – Baking soda is activated by the acid in the buttermilk, and helps your muffins brown in the oven. It adds a tiny bit of lift, but its most important task is browning.
  • Granulated sugar – Sugar adds sweetness, of course, but also tenderness to baked goods. That’s why, when you reduce the sugar, your muffins turn out tougher.
  • Butter – Melted butter adds flavor and tenderness, but not structure, so it plays a similar role here to oil, but without the greasy mouthfeel that too much oil in muffins can cause.
  • Neutral oil – Pairing melted butter with a neutral oil, like canola, vegetable, grapeseed, or peanut oils, makes your muffins super tender without making them unpleasantly oily.
  • Buttermilk – True store-bought buttermilk is thick, rich, and makes your muffins tender, tall, and super flavorful.
  • Eggs – The two eggs in this recipe add structure and form to your muffins, helping them rise to that beautiful dome.
  • Vanilla extract – Pure vanilla extract adds some depth of flavor to these otherwise simple muffins.
  • Chocolate chips – You really can use any flavor gluten free chips you like in these muffins, but I like semi-sweet the very best since they are the perfect way to offset the flavor of the buttermilk. Resist the urge to add more chips, since we want to keep them from melting together in pockets in your muffins, making these more like gf chocolate muffins (a lovely type of muffin, but a distinct one).
Pile of chocolate chip muffins in brown liners in a wire basket lined with blue and white striped towel

Tips for making the best gluten free chocolate chip muffins

How to keep the chocolate chips from sinking in these gf muffins

Mix-ins do have a habit of sinking to the bottom of muffins during baking. This is especially true of mix-ins that release moisture during baking, like blueberries in blueberry muffins.

It doesn’t happen much with chocolate chips, which soften during baking, but really don’t melt in the traditional sense. But if you’re concerned at all that your chips are going to sink, rather than being delightfully studded throughout these muffins, I have a couple tips.

Before you add the chips to the muffin batter, line the well of each muffin tin with a small dollop of plain, no-chip, muffin batter. Then, add the chips (you’ll probably want to stick with 4 ounces or less) to the remaining batter and divide it among the wells.

You can also try adding fewer chips, since they’re less likely to clump and sink together. Finally, reserve a few to sprinkle right on top of the muffin wells after you’ve already divided up the batter.

Just be sure to press those reserved chips into the muffins, or they’ll nearly fall off when the muffins are fully baked. The few chips on top also look pretty, and help them express themselves as chocolate chip muffins.

raw chocolate chip muffin batter in brown liners in 12-cup muffin tin

Bake your gf chocolate chip muffins in a hotter-than-usual oven, for less time

Baking your muffins at 375°F/190°C encourages them to rise quickly, which is what helps create that lovely muffin dome. You’ll bake them for less time, though, than you would expect (about 18 minutes is plenty).

For the best of both worlds, preheat your oven to 375°F, place your muffin tin in the oven, and then immediately reduce the temperature to 350°F. As the temperature falls, it will more gently bake the inside of your muffins without a chance of burning the outside.

Bake your muffins in a lightly colored tin

A dark muffin tin attracts too much heat too quickly in the oven, and increases the chance that the bottoms and edges of your muffins will burn. That’s especially true when your muffins are baking at 375°F.

Chocolate chip muffin with muffin liner partially peeled off on a small pewter plate and muffin basket in background

Gluten free chocolate chip muffins: substitution suggestions

How to make gluten free dairy free chocolate chip muffins

There’s a combination of a neutral oil and melted and cooled butter in these muffins. If you can’t have dairy, I don’t recommend trying to replace the melted butter with more oil.

When I tried making these muffins with all oil, the muffins looked fine, but tasted very oily to me. Instead, try using vegan butter (Melt and Miyoko’s Kitchen are my favorite brands) or even Earth Balance buttery sticks (and then reduce the salt to a pinch).

In place of buttermilk, use half nondairy milk and half plain unsweetened nondairy yogurt, each with the most neutral flavor you can find.

How to make gluten free egg free chocolate chip muffins

There are two eggs in this recipe. I think you should be able to replace each of them with a “chia egg” (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel).

How to make vegan gluten free chocolate chip muffins

You could try replacing both the dairy and the eggs in this recipe, but I’d recommend using our recipe for vegan gluten free muffins instead, which doesn’t use any “egg replacers,” but was developed to be made without them in the first place.

About the cornstarch in these gf muffins

If you can’t have corn, try arrowroot or potato starch. If you’re using a high-starch blend, like (our mock) Cup4Cup, replace the cornstarch with an equal amount, by weight, of that gluten free flour blend.

How to replace buttermilk when you’ve run out

Please don’t try replacing buttermilk in a recipe with the “trick” most people seem to love of adding some acid (vinegar or lemon juice) to milk!

The same goes (oddly) for hydrating buttermilk powder. I do love buttermilk powder for baking, but I never use it, even with added water, in place of actual buttermilk.

Store-bought buttermilk is thick and rich. Adding a bit of acid to regular milk, dairy or nondairy, just makes slightly sour-tasting milk that’s still watery.

If you don’t have buttermilk in your refrigerator, but you want to make this recipe or any other that calls for buttermilk, you can still pretty easily replace it. Just use milk and half plain unsweetened yogurt, each half of the total, by volume.

I’ve tested many of my recipes both ways, most of them in fact, and it always works almost exactly as buttermilk does. And it’s even equally applicable to nondairy substitutes.

Half of a chocolate chip muffin on a small pewter plate


How do I keep my gluten free muffins moist?

Gluten free muffin batter is quite dense, which is part of how we create that lovely, bakery-style dome on top. But that doesn’t mean your batter should ever be dry, so measure your dry ingredients carefully by weight, or you might overmeasure, and be sure your wet ingredients are at room temperature, so they combine fully.

How can I keep my gluten free chocolate chip muffins fresh after baking?

Store your baked and cooled muffins in a plastic container with a tight-fitting lid, to seal in moisture. Don’t refrigerate them at all, since that tends to dry out baked goods, and only keep them in that container on the counter for 3 days, no more.

Can I freeze my gluten free muffins for longer storage?

Yes! Once they’re completely cooled, you can freeze your muffins in a single layer on a small rimmed baking sheet, and then wrap them tightly in a freezer-safe wrap for up to 3 months. Defrost at room temperature or at lower power in the microwave for just a few moments.

How long should gluten free chocolate chip muffins cook in a mini muffin pan?

If you’d like to make these into miniature muffins, you can follow the same instructions and bake them in a light-colored miniature muffin pan (affiliate link; feel free to shop around!) for about 14 minutes, but start checking at 10 and remove them when they’re nicely domed. The last thing you want to do is overbake them.

Do I need to use muffin tin liners to bake the best gluten free chocolate chip muffins?

No, you can skip the liners and just grease your muffin tin well with a cooking oil spray. Just be sure to get in all the crevices of your muffin tin wells so your muffins don’t stick.

How to make gluten free chocolate chip muffins, step by step



Gluten Free Chocolate Chip Muffins

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A foolproof recipe for gluten free chocolate chip muffins that are always tender and moist, and have that beautiful bakery-style dome. They're lovely for breakfast or an afternoon snack, and they freeze beautifully!
Course Breakfast, Muffins
Cuisine American
Keyword gluten free chocolate chip muffins, gluten free muffins
Prep Time 10 minutes
Cook Time 18 minutes
Servings 12 muffins
Author Nicole Hunn


  • cups all purpose gluten free flour blend (I used Better Batter; please click thru for full gf flour blend info)
  • ¾ teaspoon xanthan gum omit if your blend already contains it
  • ½ cup cornstarch (See Recipe Notes)
  • teaspoons baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon kosher salt
  • ¾ cup granulated sugar
  • 4 tablespoons unsalted butter melted and cooled
  • 3 tablespoons neutral oil (canola, grapeseed, vegetable, peanut all work)
  • cup buttermilk at room temperature (See Recipe Notes)
  • 2 eggs at room temperature, beaten
  • 1 teaspoon pure vanilla extract
  • 4 ounces semi-sweet chocolate chips plus up to 1 ounce more


  • Preheat your oven to 375°F. Line the wells of a standard 12-cup muffin tin and set the tin aside.
  • In a large mixing bowl, place the flour, xanthan gum, cornstarch, baking powder, baking soda, salt, and granulated sugar, and whisk to combine well.
  • Create a well in the center of the dry ingredients, and add the melted butter, neutral oil, buttermilk, beaten eggs, and vanilla, and mix until just combined.
  • Add 4 ounces of the chocolate chips, and mix until evenly distributed throughout the batter. Stir in a few more chocolate chips if you’d like a more dense ratio of chips.
  • Fill the wells of your muffin tin about ¾ of the way full, shake the pan back and forth to distribute the batter more evenly, and/or smooth the tops with wet fingers. If there are any chips remaining, you can place them on top of the batter in the wells and press down gently to adhere.
  • Place the muffin tin in the center of the preheated oven and bake until the top of the center muffin springs back when pressed gently in the center, and it’s lightly golden brown on the edges (about 18 minutes). Do not overbake.
  • Remove the pan from the oven and remove the muffins immediately from the tin. Place them on a wire rack to cool before serving.



For cornstarch

If you’re using a higher starch all purpose gluten free flour blend, like (mock) Cup4Cup, replace the cornstarch with an equal amount, by weight, of the flour blend.

For buttermilk

If you don’t have buttermilk, you can always substitute it with half plain unsweetened yogurt (not the Greek kind) and half milk, by volume. Dairy or dairy-free.

Originally published on the blog in 2021; in 2022, a lot more text resources added to help ensure success, recipe tweaked slightly to ensure a lovely muffin dome.

Words gluten free chocolate chip muffins with images of Chocolate Chip Muffins in a pile in a wire basket, in a muffin tin, and one muffin cut in half on a small pewter plate

The post The Best Bakery-Style Gluten Free Chocolate Chip Muffins appeared first on Gluten Free on a Shoestring.

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