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These gluten free chocolate muffins are tender and chocolatey, but clearly muffins and not cupcakes, so enjoy them first thing in the morning, guilt-free! Since they're made without butter, they're also easily made dairy free, too.

“I made these yesterday, and they were fabulous! The texture was great, and the taste was nice and chocolatey without being too sweet. Thanks for a great recipe!”
My Pro Tip
Why you'll love this recipe
Between the melted dark chocolate in the batter, and the mixture of a neutral oil and rich cocoa powder, these gluten free chocolate muffins are super moist, tender, and richly satisfying. These are not the sort of muffins you want to offer to someone who doesn't love chocolate, though!
But assuming you have an audience of chocolate fans, these muffins will not disappoint. They're made easily by mixing together all the wet ingredients, from melted chocolate through to buttermilk, first, then mixing them into the few dry ingredients until just combined.
We start the baking with some extra heat to coax that chocolate batter up into a craggy dome with lots of muffin-top texture, then reduce it almost right away so nothing burns. Since these muffins are so dark and rich, you wouldn't know your muffins were burning in a too-hot oven until it was too late to save them!
what's in it
Recipe ingredients
- Baking chocolate – The baking chocolate that is melted and mixed into this chocolate muffin batter can be dark (which usually contains between 50% and 90% cocoa solids, in addition to cocoa butter and sugar) or semi-sweet (a type of dark chocolate, one that is usually toward the lower end of cocoa solids and less sugar than milk chocolate). Melt it gently in a double boiler or in a microwave at reduced power so it doesn't burn or seize.
- Neutral oil – Rather than baking with butter, like we do in our classic mix-in gluten free muffin recipe, we are using oil as fat here since it has less moisture and keeps the muffins more moist. You can use any plain oil with a neutral flavor, like canola, vegetable, grapeseed, or peanut oil.
- Unsweetened cocoa powder – I use Rodelle brand Dutch-processed cocoa powder for its extra richness, but natural cocoa powder works fine here, too.
- Sugars – Using half granulated sugar and half light brown sugar adds tenderness, extra moisture, and of course sweetness.
- Egg – Using one single egg helps keep these muffins moist and tender without the dryness that too much egg white in the batter can create.
- Buttermilk – Commercial buttermilk has thickness and richness that helps tenderize and moisten this chocolate muffin batter. Don't replace it with plain milk that's been soured with a little lemon juice or vinegar, which won't do the same for your muffins. You can replace it with half plain yogurt or sour cream, half 2% or whole milk, by volume, though. Plain kefir yogurt is also a great buttermilk substitute.
- Gluten free flour blend – Be sure to use a well-balanced, smooth, reliable gluten free flour blend. Any of my recommended all purpose gluten free flour blends will work. Be sure to add xanthan gum in the amount specified in the recipe if your blend doesn't already contain it.
- Baking powder – Baking powder is double-acting, which means that it is activated when it gets hydrated by being adding to liquid in the recipe, and again in the oven. It provides rise and lift in these muffins.
- Baking soda – Baking soda also provides some lift, but it's also responsible for helping to brown your muffins in the oven. Plus, if you are using natural cocoa powder, it will neutralize the additional acid in your cocoa.
- Salt – Salt helps balance sweetness, and brings out the chocolate flavor of these muffins.
- Chocolate chips – I like to use semi-sweet chocolate chips, but if you know that you're serving your muffins who can only abide the darkest of chocolate, try using dark chocolate chips. Or switch it up and use white chocolate chips or even peanut butter or butterscotch chips (just make sure they're gluten free, though, since some are not!).
How to make gluten free chocolate muffins
The batter for these chocolate muffins is thick, but soft. It isn't the sort of batter that you're going to pour into the wells of a muffin tin. Instead, you'll scoop it and shake it into an even layer, then bake it.
Combine the dry ingredients, then wet
- In a large mixing bowl, whisk together the dry ingredients (all purpose gluten free flour with xanthan gum, baking powder and soda, salt, and cocoa powder).
- In a separate bowl, melt chopped chocolate, taking care not to burn it.
- Add oil to the melted chocolate, then granulated and light brown sugars, an eggs, buttermilk and vanilla, and whisk well.
Finish the batter
- Add the wet chocolate mixture to the dry ingredients, and mix to combine. The batter will be thick and soft.
- Mix in the chocolate chips.
Bake high, and then lower
- Transfer the batter to a muffin tin. The wells should be almost completely full of batter
- Bake at 375ยฐF for 5 minutes, then lower the oven temperature to 350ยฐF for the rest of the baking time (about 14 minutes more).
My Pro Tip
Expert tips
Use an oven thermometer during baking
Most ovens drift out of calibration, and rather than paying to have them calibrated regularly, just use a simple, inexpensive analog oven thermometer to gauge your oven's temperature. If your oven runs hot here, these muffins are so dark in color that you won't know they're beginning to burn until it's too late.
Turn the oven temperature down after the first 5 minutes
The reason to start baking at 375ยฐF, which is higher than the usual cake-baking temperature of 350ยฐF, is to encourage your muffins to rise quickly at the start. That's how you get a nice, round dome on top. After those first 5 minutes, though, turn the temperature down 25ยฐF, to 350ยฐF to finish baking or your muffins may burn.
Fill muffin wells all the way
All muffin tin wells have different sizes and even shapes. There's just no way to know for sure exactly how much batter you'll need to fill your muffin wells unless we're all using my same basic Wilton 12-cup standard muffin tin.
So be sure to fill your wells all the way, and if your muffin tin is larger than most and you can't make a full 12 muffins, it's worth making fewer muffins with the big dome than more, smaller ones!
substitutions
Ingredient substitutions
Dairy free
The dairy in these muffins is in the form of buttermilk, and possibly chocolate. Most dark or even semi-sweet baking chocolate will be dairy-free and gluten-free, but check labels and make phone calls if necessary to be sure.
In place of buttermilk, you can use half non-dairy plain yogurt or sour cream and half unsweetened nondairy milk, by volume. You can also use that combination with dairy if you can have dairy, but don't happen to have buttermilk on hand.
Egg free
There's only 1 egg in this recipe, so it should transition easily to being egg-free. Try using one “chia eggs.” One “chia egg” is made by combining 1 tablespoon ground white chia seeds with 1 tablespoon lukewarm water. Mix in a small bowl and allow the mixture to sit until it gels. A “flax egg” should work, too.
FAQs
Muffins and cupcakes are all baked in muffin tins, so you're naturally going to compare them to one another! These are muffins, not cupcakes, though, since they have a more dense, somewhat tighter crumb with an irregular top with lots more texture than a smooth, gluten free chocolate cupcake top that's ready for frosting. Muffins are usually less sweet than cupcakes, since they're for gluten free breakfast after all!
No! You can use a cooking oil spray to grease the wells of your muffin tin instead of using liners. I usually prefer to use greaseproof liners, though, since no muffin tin is perfect, and especially as they age, they tend to have spots to which the batter will stick no matter how well you grease the tin. And that can lead to a muffin that's stuck to the tin and simply can't be removed without breaking it into pieces.
Yes! You can leave out the chips entirely, replace them with another flavor of chips like gluten free peanut butter chips, or with an equal amount, by weight, of chopped soft nuts. Raw walnuts or pecans would be great!
Since these muffins are dark in color, it can be more difficult to tell when they're done baking, and they can burn if you're not careful. We start out baking at a higher temperature to get the muffins to rise high into a dome like muffins from a bakery. Then, we continue to bake at a lower temperature until the top of the center muffin feels firm and a toothpick inserted in the center has no more than a few moist crumbs attached.
I haven't tested these muffins with an alternative sugar, but I think they would work with Lankato brand monkfruit brown sugar alternative and white sugar alternative. You may need to add a bit more moisture to get the proper texture in the raw batter, since they can be drying. Try adding a bit of water if the raw batter seems too stiff. Be sure to use sugar-free baking chocolate and chocolate chips, too. Lily's is a great brand.
make ahead/leftovers
Storage instructions
These muffins stay fresh at room temperature, if wrapped individually with plastic wrap or in a sealed container, for up to 3 days. Just be sure to let them cool completely first so they don't collect moisture.
Freezing
For longer storage, freeze them in a freezer-safe container or wrap for up to 3 months. The less air they come in contact with in the freezer the better, since that's what leads to freezer burn.
Refreshing
To enjoy muffins you've frozen, defrost one at a time at room temperature for 30 minutes or in the microwave for 25 seconds. Sprinkle lightly with lukewarm water and place in the toaster oven on toast or at 300ยฐF for 5 minutes to refresh.
Gluten Free Chocolate Muffins Recipe
Ingredients
- 1 ยพ cups (245 g) all purpose gluten free flour blend, (please click thru for full info on appropriate blends)
- 1 teaspoon xanthan gum, (omit if your blend already contains it)
- 1 teaspoon baking powder
- ยพ teaspoon baking soda
- ยผ teaspoon kosher salt
- ยฝ cup (40 g) unsweetened cocoa powder, I prefer Dutch-processed, but natural cocoa powder works, too
- 4 ounces dark or semi-sweet baking chocolate, chopped
- 6 tablespoons (84 g) neutral oil, canola, grapeseed, vegetable, peanut oils all work
- ยฝ cup (100 g) granulated sugar
- ยฝ cup (109 g) packed light brown sugar
- 1 (50 g (weighed out of shell)) egg, at room temperature
- 1 cup (8 fluid ounces) buttermilk, at warm room temperature
- 2 teaspoons pure vanilla extract
- 6 ounces semi-sweet chocolate chips
Instructions
- Preheat your oven to 375ยฐF. Grease or line a standard 12-cup muffin tin with muffin liners, and set it aside.
- In a large mixing bowl, place the flour blend, xanthan gum, baking powder, baking soda, salt, and cocoa powder, and whisk to combine well.
- In a separate medium-size, heat-safe bowl, place the chopped chocolate and place over a small pot of simmering water, making sure the water in the pot doesnโt touch the bowl. Melt the chocolate, stirring occasionally, until smooth.
- Remove the melted chocolate from the heat, add the oil and whisk until smooth.
- To the chocolate mixture, add the granulated sugar and the brown sugar, and whisk to combine. Break up any lumps in the brown sugar.
- Crack the egg open into the chocolate mixture, and whisk the egg into the mixture until smooth.
- Next, add the buttermilk and vanilla, and whisk again until smooth. The mixture will be thin.
- Create a well in the center of the dry ingredients, add the entire chocolate mixture, and mix until just combined. The batter will be thick but should be relatively shiny and soft.
- Mix in the chocolate chips. You can reserving a few chips to scatter on top of the muffin batter in the wells of the muffin tin, if you prefer.
- Divide the raw muffin batter among the wells of the muffin tin. Each well should be filled or nearly filled with batter.
- Top with any reserved chocolate chips, and press them down gently so they aren't just sitting on top of the batter.
- Place the tin in the center of the 375ยฐF preheated oven and bake for 5 minutes.
- Reduce the oven temperature to 350ยฐF, and continue to bake for about 14 minutes, or until the muffin tops are firm to the touch and a toothpick inserted in the center of the middle muffin comes out with no more than a few moist crumbs attached. Do not overbake or the muffins may burn.
- Remove from the oven and allow to cool in the tin for 5 minutes before transferring to a wire rack to cool completely.
Video
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
I am a huge chocolate lover, but I just made these, followed exactly (but used fewer chips then called for at the end), and franklyโฆ it was WAY TOO chocolatey! I think I will crumble them up and use as topping on plain yogurt.
They really are for chocolate lovers, JC. It sounds like a chocolate muffins wasn’t the best choice, then!
I made them this morning with substitutions. I only had unsweetened baking chocolate so I used that and added additional sugar. I substituted unsweetened applesauce for the oil and Truvia brown sweet complete for the brown sugar. I also cut back to 4 ounces on chocolate chips (used Lily’s sugar free of course). Plus I made 18 muffins. They turned out great.
I have baked these muffins two times now and both times the top has separated from the muffin. Do you have any idea why this would happen? What did I do wrong?
It sounds like you may be overfilling your muffin wells. Muffin tin wells are not standard, so some tins have more shallow wells and canโt accommodate enough batter so youโll have to make more than 12 muffins. And as always please look at any ingredient substitutions, and gauge your ovenโs temperature independently with a standalone oven thermometer as most ovens run hot which could create an unstable dome as the muffin rises too fast.
Wonderful