Gluten Free Lemon Cupcakes | Lemon Glaze

Gluten Free Lemon Cupcakes | Lemon Glaze

These gluten free lemon cupcakes have the tender crumb of the best vanilla cake, and they’re packed with lemon flavor. For lemon lovers only!

Lemon cupcake on plate with other plate in background

Creaming the butter and sugar

Creaming the butter and sugar in this cupcake batter is essential to making a tender cake that is light, and never greasy. You want to whip them together until the color is pale yellow, and then again after adding the eggs.

That way, you’ll create just enough air bubbles in the batter, and the cupcakes will hold onto them during and after baking. When making cookies, I rarely cream the butter and sugar, since I typically want my cookies to be chewy.

Lemon cupcake batter in mixing bowl

A thick glaze that doesn’t disappear into the cupcakes

Rather than frosting, these gluten free lemon cupcakes have a simple lemon sugar glaze instead thick frosting. The glaze helps to seal in the moisture in the cupcakes, and easily adds a really nice punch of lemon flavor.

Most of the time that you see a glaze on cupcakes and cakes, it’s made with confectioners’ sugar, and a liquid. But there are a couple secrets to ensuring that the glaze stays thick, rather than disappearing into whatever cake it’s served on.

First, your baked goods must be completely cool before glazing them. Any residual heat in the cake or cupcakes will melt the glaze. By the time everything cools, the glaze will have slipped right off.

Second, add your liquid very, very slowly. Begin with just enough liquid to make a paste that’s hard to stir. Then, add more liquid by the drop, mixing vigorously to combine.

You will be amazed by how much of a difference a bit of liquid makes. You want a very slowly, thickly pourable glaze. If you add too much liquid, you can add more confectioners’ sugar to thicken but it’s much harder than slowly thinning a paste.

Lemon cupcakes three on a plate

Can I make these cupcakes other flavors?

These lemon cupcakes are relatively similar to vanilla cupcakes with lemon flavor, but they’re not just a version of the same recipe. Their tender crumb is important, but the flavor is what’s most prominent.

If you’d like to try them with a different flavor, I recommend trying a different type of citrus. I think they’d be great with lime zest and lime juice, too. I might use a bit less, though, since lime zest tends to be a bit more bitter than lemon zest.

You could also try using blood oranges or navel oranges. Resist the urge to use anything other than fresh-squeezed juice, though. Baking intensifies flavors, and you want your citrus flavors to be bright, not bitter.

Lemon cupcakes batter raw in muffin tin

Ingredients and substitutions


To replace the dairy in these cupcakes, you’ll need a substitute for both the butter and the sour cream. I think you can do both, but I haven’t tried so these are just educated guesses.

In place of the butter, I recommend either Melt brand or Miyoko’s Kitchen brand vegan butter. They will become fluffy like dairy butter when beaten with sugar. Earth Balance buttery sticks might work, but they have a lot of moisture.

In place of the sour cream, you can use your favorite brand of dairy-free sour cream. If you can’t find dairy-free sour cream, try using dairy-free plain yogurt. Daiya brand is really good.


Since there are two eggs in this recipe, you should be able to use an egg replacer for each. My favorite is a “chia egg.” For each, place 1 tablespoon ground white chia seeds and 1 tablespoon lukewarm water in a bowl, mix and allow to sit until it gels.


Gluten free lemon cupcakes closeup image

Gluten free lemon cupcake batter in a bowl, and baked and glazed cupcake on a plate

Like this recipe?

Prep time: Cook time: Yield: 12 cupcakes


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

1 cup (200 g) granulated sugar

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

1 1/2 teaspoons vanilla extract

1 1/2 cups (210 g) all purpose gluten free flour (I used Better Batter)

3/4 teaspoon xanthan gum (omit if your blend already contains it)

1 1/2 teaspoons baking powder

1/2 teaspoon kosher salt

Juice and zest of 1 lemon (reserve 1 tablespoon juice for the glaze)

1/2 cup (113 g) sour cream, at room temperature

1 cup (115 g) confectioner’s sugar

More lemon zest for sprinkling (optional)


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

  • In a large bowl, place the butter and sugar, and beat until light and fluffy. Add the eggs, vanilla, lemon zest, and juice (reserving the final 1 tablespoons of juice for the glaze), and beat to combine. Add the flour, xanthan gum, baking powder, and salt, and mix to combine. Add the sour cream to the batter and mix until just combined. The batter will be light and fluffy, but not thin.

  • Divide mixture evenly among the muffin cups and shake into an even layer in each well of the pan. Place in the center of the preheated oven and bake for about 20 minutes, or until a toothpick inserted into the center comes out clean.  Remove the pan from the oven and allow the cupcakes to cool for about 5 minutes before transferring to a wire rack to cool completely.

  • Once the cupcakes are cool, make the glaze. Place the confectioners’ sugar in a medium-size bowl and add about 1 1/2 teaspoons of the reserved lemon juice. Mix until you have a very smooth, thick paste. Add more lemon juice until you have a very thickly pourable glaze. Add the liquid slowly, because it’s much easier to thin it than to thicken if once you’ve added too much liquid. Pour or spoon the glaze over the cooled cupcakes, or dip the tops in the glaze. Sprinkle with the optional additional zest, and allow to set at room temperature.

  • Recipe originally published on the blog in 2009 (!). All photos, video, text new. Recipe instructions rewritten for clarity.


  • Taylor
    July 17, 2020 at 12:51 AM

    Can you convert this to a cake recipe easily? I made the cupcake recipe and it turned out amazing but I want to make a lemon cake just like the cupcakes for my mom’s birthday (she is also gf). Would you recommend the same amounts for ingredients?

    • Nicole Hunn
      July 17, 2020 at 7:34 AM

      I don’t recommend that, no, Taylor. But I have a couple recipes for lemon cakes (one with blueberries, one without). Please use the search function!

  • Kathryn
    June 22, 2020 at 10:52 AM

    So good! My husband, brother, and sister in law would have had no idea they were gluten free if they didn’t already know. I am so happy with how they turned out!

    • Nicole Hunn
      June 22, 2020 at 12:09 PM

      That’s great to hear, Kathryn! Thank you for letting me know that happy news. :)

  • Dorrie Berkowitz
    June 19, 2020 at 9:58 AM

    Yes, Nicole, I did use Greek yogurt. It’s really the only kind I like! BTW, making these again for Father’s Day. Perfectly refreshing for what’s going to be a humid afternoon. :-)

  • Dorrie Berkowitz
    June 16, 2020 at 4:47 PM

    These were delicious! I subbed plain yogurt for the sour cream because that’s what I had in the fridge. Fabulous. I had to bake them almost 30 minutes rather than the 20 minutes in the recipe (and I do have an oven thermometer) until the cake tester came out clean.

    Loved the glaze — just the right balance of sweet and tart!

    • Nicole Hunn
      June 16, 2020 at 5:33 PM

      A better substitute for sour cream is Greek-style yogurt, Dorrie. Plain yogurt has a lot more moisture, which is why they took a lot longer to bake. So glad you enjoyed them anyhow!

  • Pamela
    June 8, 2020 at 9:31 PM

    It says juice and zest from 1 lemon and to reserve 1 tablespoon for the glaze. Since lemons vary in size and amount of juice, can you tell me about how much lemon juice you put in the cupcakes?

    • Nicole Hunn
      June 9, 2020 at 8:51 AM

      Lemons do vary in size, and typically have between 3 and 4 tablespoons of juice. That isn’t a significant enough difference to matter in this recipe since the lemon juice is just a small enough amount for flavoring. I’ve made this recipe many times over the years, using anywhere between 2 and 3 tablespoons in the cupcake batter, and never had a problem.

  • Kay
    June 7, 2020 at 9:38 PM

    This sounds delicious! My mom is gf and this site has been a godsend and makes it soo easy for me to celebrate her by baking tasty things :)

    • Nicole Hunn
      June 8, 2020 at 8:22 AM

      That’s really lovely, Kay!

  • Suzy Quigley
    June 7, 2020 at 7:02 PM

    I just made some today. A Wonderful Cup Cake. Easy but Fancy.

    • Nicole Hunn
      June 7, 2020 at 7:12 PM

      Easy but fancy is a great way to describe there, Suzy! So glad you enjoyed them.

  • Cari
    June 7, 2020 at 6:59 PM

    My daughter made these for a friend a few weeks ago. They were such a hit, she made a double batch this weekend and used the glaze on half and made lemon butter cream on the other. The are amazing! We use Bob’s Red Mill GF 1 to 1 Baking Flour.

  • Deana L Johnson
    June 7, 2020 at 1:27 PM

    Can I freeze these?
    Thank you,

    • Nicole Hunn
      June 7, 2020 at 2:07 PM

      Yes, absolutely, Deana! Good question. I would freeze them without the glaze, then defrost and glaze before serving.

  • Mary Kay
    June 7, 2020 at 12:16 PM

    Sounds great! Will try these next … I just put the bakery style blueberry muffins in the oven, at my GF husband’s request! They are a hit with us!

    • Nicole Hunn
      June 7, 2020 at 2:08 PM

      Lucky man, your husband, Mary Kay!

  • Didi
    June 5, 2020 at 3:58 PM

    These will be my next bake, I love all your lemon cakes, no, I love all your cakes💕

    • Nicole Hunn
      June 5, 2020 at 5:51 PM

      Thank you, Didi!

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