Gluten Free Chocolate Chip Muffins

March 17, 2021
At a Glance


If you want a simple gluten free chocolate chip muffin with a tender crumb, put down that overpriced boxed mix. Here’s how to make them from scratch.


Prep / Cook Time

10 minutes / 20 minutes


 5/5 (5 votes)
Gluten Free Chocolate Chip Muffins

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.

Six chocolate chip muffins in a muffin tin with one on its side

What makes this recipe 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 is traditional.

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.

Pile of chocolate chip muffins in brown liners in a wire basket lined with blue and white striped towel

How to keep the chocolate chips from sinking

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

How to replace buttermilk when you’ve run out

If you knew me in life, you’d see that I’m not shy about expressing my opinions—although I do know when to stay silent. But since this is my very own recipe blog, on my own block of the Internet, there are a few cornerstone concepts that I will push and push.

I want you to have success, and that means not just that a recipe looks like it worked. I want it to actually taste great, too.

So it is in this tradition that I beg you, 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. No doubt, it has additives that make and keep it that way, but that’s what we’re going for.

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 half milk and half plain unsweetened yogurt, by volume.

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

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

Ingredients and substitutions


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 or even Earth Balance buttery sticks (and then reduce the salt to a pinch).

In place of buttermilk, use half milk (nondairy is fine) and half plain unsweetened yogurt (again, nondairy is fine).


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).


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

Half of a chocolate chip muffin on a small pewter plate

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

Like this recipe?

Prep time: Cook time: Yield: 12 muffins


1½ cups (210 g) all-purpose gluten free flour (I used Better Batter)

¾ teaspoon xanthan gum (omit if your blend already contains it)

½ cup (70 g) cornstarch (See Recipe Notes)

1½ teaspoons baking powder

¼ teaspoon baking soda

½ teaspoon kosher salt

¾ cup (150 g) granulated sugar

4 tablespoons (56 g) unsalted butter, melted and cooled

3 tablespoons (42 g) neutral oil (canola, grapeseed, vegetable, peanut)

½ cup + 2 tablespoons (5 fluid ounces) buttermilk, at room temperature (See Recipe Notes)

2 eggs (100 g, weighed out of shell) at room temperature, beaten

1 teaspoon pure vanilla extract

4 to 5 ounces semi-sweet chocolate chips


  • Preheat your oven to 325°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 20 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.


  • Amanda Farr
    May 6, 2021 at 1:43 PM

    Hello there – thank you for your lovely recipes. I am currently looking for a recipe for gluten free vegan chocolate cupcakes. I have tried a couple of recipes but they always seem to be dry. Would really appreciate your help :)

    • Nicole Hunn
      May 6, 2021 at 2:01 PM

      Hi, Amanda, you can always use the search function on the blog to find any recipe that I have in my archives. It’s very robust and helpful. I don’t have a recipe for vegan chocolate cupcakes, specifically, but search for “crazy cake,” which is a vegan chocolate cake, and you should be able to use that batter for cupcakes.

  • Denise Sheppard
    March 28, 2021 at 12:02 PM

    Made these yesterday with my niece! They are outstanding…best gf muffin I have had. Warmed 2 leftover for breakfast today and they were still moist and very tasty.. this recipe is a “keeper” for both of us!

    • Nicole Hunn
      March 28, 2021 at 12:33 PM

      That’s awesome to hear, Denise! My freezer is often stocked with these for my kids to rewarm on a busy morning!

  • Thea Sugarman Lee
    March 21, 2021 at 11:43 AM

    I know you said not to use the dried buttermilk. What if I use the dried buttermilk with half-and-half, instead of water? Do you think that would work OK? I am a homebound, ambulatory wheelchair user. I don’t often have access to quick trips to the store. I’m trying to find a balance.

    • Nicole Hunn
      March 21, 2021 at 12:17 PM

      I really sympathize, Thea. I think buttermilk with half and half is definitely worth trying. And when you are able to, try keeping some plain unsweetened yogurt on hand in addition to milk, since together they’re a perfect buttermilk sub.

  • Marji Jochums
    March 21, 2021 at 10:08 AM

    I made these muffins with mock better batter and half Greek yogurt/half milk combo–delicious! Thanks for the recipe.

    • Nicole Hunn
      March 21, 2021 at 10:32 AM

      That’s great, Marji!

  • Rosemary
    March 17, 2021 at 9:55 PM

    Just made these with lactose-free yoghurt and lactose-free milk instead of buttermilk. They are absolutely delicious! Thank you!

    • Nicole Hunn
      March 18, 2021 at 9:47 AM

      That’s awesome, Rosemary! I’m thrilled you used my favorite buttermilk substitute successfully. Friends don’t let friends use bad buttermilk. 🙂

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