Gluten Free Cinnamon Roll Cupcakes

October 28, 2020
At a Glance


Classic vanilla cupcakes with a cinnamon swirl in the center and on top, these gluten free cinnamon roll cupcakes have all the taste of the classic roll, but baked in a muffin tin. Top with a classic or rich glaze, or nothing at all.


Prep / Cook Time

10 minutes / 19 minutes


 5/5 (33 votes)
Gluten Free Cinnamon Roll Cupcakes

Moist and tender gluten free cinnamon roll cupcakes have all the flavor of the best cinnamon roll, made quick and easy in a muffin tin.

Cinnamon roll cupcake cut in half facing forward with frosting on one half

The flavor that unites us

You know how some people are chocolate people, and others are vanilla people? Well, almost everyone is a cinnamon-sugar person (I’m sure some of you hate the stuff, but I’ve yet to hear about it—and readers aren’t usually shy about sharing what they don’t like!).

We have plenty of recipes for cinnamon rolls here on the blog, but there is rolling and shaping involved in every single one of them. These gluten free cinnamon roll cupcakes are for those times when you just can’t be bothered to roll and shape! 

The tops have a lightly crunchy cinnamon-sugar crust, and the cake is tender and buttery and not-too-sweet. Inside, there’s a perfect cinnamon-sugar swirl. But I promise it’s simple to do.

Overhead image of raw cinnamon roll cupcake batter in muffin tin

How do you make the cinnamon swirl?

The cinnamon swirl is a simple mixture of melted shortening or coconut oil, brown sugar, and cinnamon. Rather than mixing it into the cupcake batter, where it would change the consistency of the cakes, we place half of it in the center and half on top.

We begin by filling the muffin tins halfway full with the plain batter. That creates a solid base for baking. Then, we add half the cinnamon-sugar filling mixture, and swirl it around a bit to make sure it doesn’t just leak out during baking.

On top, we add the remaining plain cupcake batter, and the final swirl mixture. It takes just a few moments, and it’s the reason we’re not rolling and shaping cinnamon roll dough.

Of course, if you’d prefer an actual cinnamon roll, I’d begin with our yeast free gluten free cinnamon roll recipe. It’s the next easiest thing to these cupcakes.

A close up of cinnamon roll muffin on a metal tray

What are the options for the glaze?

Since the cinnamon sugar on top creates a very light and crispy glaze, these cupcakes can be served plain. Since plain here isn’t really plain at all, and if you’re storing them for later use, you’ll want to leave them unglazed (see further discussion below).

In about half of the photos, like the one just below, you’ll find a simple white confectioners’ sugar glaze being spooned on top. It’s made by mixing a tiny bit of milk into confectioners’ sugar, and it’s delicious in its simplicity.

If you’d like a more spreadable, richer glaze, you can add butter and cinnamon to the confectioners’ sugar. Add water by the drop to create a paste with the consistency of frosting.

If you’d like to serve this glaze on top of the cupcakes, try spooning it over them while they’re still a bit warm from the oven. Otherwise, slice the cupcakes in half and spoon the glaze on each half.

A close up of food cinnamon roll muffin with white sauce being drizzled over it

Can you store the cupcakes after baking?

These gluten free cinnamon roll cupcakes are so moist and tender, and the cinnamon is so fragrant, that you’ll have to enjoy at least one right away. But if you don’t plan to serve them all right away, they’re easily stored for another time. Simply glaze only the cupcakes you plan to serve right away.

If you don’t plan to serve them all right away, freeze them unglazed. Wait until all of the baked cupcakes are completely cool, then freeze them in a single layer.

When you’re ready to serve them, just allow them to defrost at room temperature or even in the microwave for a few seconds. You can even refresh them in a toaster oven at about 300°F to crisp that cinnamon sugar on top. Then, make the glaze fresh and serve.

Cinnamon roll cupcake cut in half on white plate with cinnamon frosting on small spoon

Ingredients and substitutions


There is dairy in these cupcakes in the forms of butter and buttermilk. The butter in the muffin batter can be replaced with your favorite vegan butter replacement. My favorites are Melt brand and Miyoko’s Kitchen brand vegan butter.

In place of buttermilk, use half non-dairy plain yogurt (I like So Delicious brand) and half unsweetened nondairy milk (my favorite is unsweetened almond milk). This substitute also works with dairy yogurt and milk, if you can have dairy but you’ve run out of buttermilk.


There are 3 whole eggs in this recipe. For that reason, I don’t believe that my usual suggestion of a “chia egg” for each egg would work. For reference, a “chia egg” is one tablespoon ground white chia seeds mixed with one tablespoon lukewarm water, mixed and allowed to gel.

If you are willing to create a boiled flax egg (by boiling ground flax seeds with water until a viscous liquid is produced, then straining out the seeds), that might work. 

Vegetable Shortening

The vegetable shortening in the swirl/filling can easily be replaced with virgin coconut oil. I don’t recommend using butter, which solidifies too quickly and will make it more difficult to swirl into the cupcake batter.


cinnamon roll muffins in muffin tray

Cinnamon Roll Cupcake sliced in half on a white plate with frosting and raw cupcake batter in a muffin tinMoist and tender gluten free cinnamon roll muffins are like the best cinnamon bun you've ever tasted—but made quick and easy in a cupcake tin.

Like this recipe?

Prep time: Cook time: Yield: 12 cupcakes


For the swirl/filling
4 tablespoons (48 g) vegetable shortening, melted and cooled

1/4 cup (55 g) packed light brown sugar

1 teaspoon ground cinnamon

For the cupcakes
2 cups (280 g) basic gum-free gluten free flour blend (185 grams superfine white rice flour + 61 grams potato starch + 34 grams tapioca starch) (See Recipe Notes)

1/2 teaspoon xanthan gum (See Recipe Notes)

1 teaspoon baking powder

1/2 teaspoon baking soda

1/2 teaspoon kosher salt

8 tablespoons (112 g) unsalted butter, at room temperature

3/4 cup (150 g) granulated sugar

3 eggs (150 g, weighed out of shell) at room temperature, beaten

2 teaspoons pure vanilla extract

2/3 cup (158 ml) buttermilk, at room temperature

For the glaze (See Recipe Notes)
3/4 cup (86 g) confectioners’ sugar

1 to 2 teaspoons milk (any kind, including nondairy)


  • Preheat your oven to 350°F. Grease or line a standard 12-cup muffin tin, and set it aside.

  • First, make the swirl/filling. Place the melted shortening in a small bowl, and add the brown sugar and cinnamon, then mix to combine well. Set the bowl aside.

  • Make the cupcake batter. In a medium-size bowl, place the flour blend, xanthan gum, baking powder, baking soda, and salt, and whisk to combine well. Set the dry ingredients aside. In the bowl of a stand mixer (or a large bowl with a handheld mixer), beat the butter on medium speed until light and fluffy. Add the granulated sugar, and then the eggs and vanilla, beating on medium speed after each addition until well-combined. Add the dry ingredients, alternating with the buttermilk, in 3 parts, beginning and ending with the dry ingredients. The batter will be thick but light and fluffy.

  • Place half of the cupcake batter in the prepared wells of the muffin tin, and top with half the filling. Swirl the filling around gently in the batter with the short end of a chopstick, or a toothpick or skewer. Top with the remaining cupcake batter, and then the remaining filling, and swirl again. Shake the tin back and forth until the batter sits in an even layer in each muffin well.

  • Place in the center of the preheated oven and bake for 19 minutes, or until a toothpick inserted in the center comes out clean. Do not over-bake. Remove the cupcakes from the oven and allow to cool in the tin for 10 minutes before transferring to a wire rack to cool completely.

  • While the cupcakes are cooling, make the glaze. In a small bowl, place the confectioners’ sugar and 1 teaspoon of the milk, and mix to combine well. You should have a smooth, but very thick paste. Add more milk by drop and mix well until you have a thick, but slowly pourable, glaze. Pour a bit of glaze over each cooled cupcake. Serve immediately.

  • Originally published on the blog in 2014. Some photos, video, and alternative glaze new. Recipe otherwise unchanged.


Where should I send your free guide?

By entering your email, you're agreeing to our Privacy Policy. We respect your email privacy, and will never share your information.