Simple and delicious, these fluffy gluten free lemon cupcakes are a delicious dessert for lemon lovers. Top them with either lemonade icing or frosting for any celebration! These cupcakes are also dairy-free so that everyone can enjoy them!

Three lemon cupcakes on a plate. They are frosted and topped with lemon sprinkles.

These lemon gluten free cupcakes are incredible and are a delicious way to use some of my fresh lemons. If you love that sweet-tart flavor you get from lemons, you will love this simple, gluten free lemon cupcakes recipe!

This is one of my favorite cupcake recipes. For more lemon recipes, try my Gluten Free Lemon Pound Cake recipe! For more cupcake recipes, check out all of my Gluten Free Cupcakes.

A picture of the lemon tree in our backyard.
Here is our tiny but mighty lemon tree!

Why These gluten free lemon cupcakes are the best:

  1. This gluten free lemon cupcake recipe is homemade, made from scratch, and bursting with fresh lemon flavor. If you want a tried and true cupcake recipe, this is it!
  2. These cupcakes are also dairy-free!
  3. Store-bought gluten free cupcakes will never be as good. I made this cupcake recipe easy to follow so that you can make these in your kitchen!
  4. You can top these with the lemonade icing or add a few drops of yellow food coloring to my easy gluten free frosting recipe! Also, be sure if you use sprinkles to check my gluten free sprinkles list to verify the brand you use is gluten free!

These were super delicious! I made it into a cake instead of cupcakes!”

chronically gluten-free, pinterest comment

Allergen Information:

This gluten free lemon cupcake recipe is gluten-free, dairy-free, nut-free, and soy-free.


  • Make these cupcakes gum-free (aka gluten free lemon cupcakes without xanthan gum) using my DIY Gluten Free Flour Blend. It uses psyllium husk instead of xanthan gum as a binder.
  • If you can’t have coconut, swap the coconut oil for another oil like avocado or canola oil.
  • If you are dairy-free, use plant-based butter (aka margarine) for the frosting.
Photos of the lemon cupcake ingredients.

Ingredient Notes:

  • Gluten-Free Flour Blend—I tested this recipe using Bob’s Red Mill 1:1 Gluten-Free Flour Blend and King Arthur’s Measure for Measure Gluten-Free Blend. That doesn’t mean other flour mixtures will not work; I just have not tested other flour.
  • Xanthan Gum – If your gluten free flour blend doesn’t contain xanthan gum or guar gum, please add 1 teaspoon. See the Substitutions section above for a gum-free alternative.
  • Eggs – Use large eggs. You can use them from the refrigerator; they do not need to be at room temperature. Note I have not tested this recipe with any egg replacer.
  • Sugar – You can use organic or regular. Both work perfectly fine.
  • Lemons – I prefer fresh, but bottled is okay to use. If you have a lemon tree like me, use fresh!
  • Non-Dairy Milk – I used almond milk, but you can also use a different one, like flaxseed or soy milk. I do not recommend canned coconut milk. Oat milk is great to use, but check to see is oat milk gluten free.
  • Coconut Oil – Any brand is fine; depending on the temperature in your house, be sure to melt it before using it. You can also use another light oil type like canola.
  • Vanilla Extract – Use pure vanilla extract.
  • Baking Soda – I use baking soda because it works better in acidic recipes.
  • Powdered Sugar – You can use this for the yummy lemonade glaze recipe below or in a homemade buttercream frosting.

If you love fruity cupcakes, try my Gluten Free Peach Cupcakes recipe!

Step-By-Step Photos and Directions:

Making these fluffy gluten free lemon cupcakes is so easy. Preheat your oven to 350º F, and move your oven rack to the middle position. You do not want your oven rack too low, or your cake bottoms can burn.

A photo of the dry ingredients in a large mixing bowl.

Step 1: Add your gluten free flour, sugar, baking soda, and salt to a large mixing bowl. Use a whisk to blend dry ingredients together.

To measure your gluten free flour, I recommend using either the spoon method or the leveling method.

Spoon Method: You can also use a spoon to fill the measuring cup. Use a knife to level along the top to remove the extra flour. Leveling Method: Put the measuring scoop into the flour and fill. Do not pack the flour. Use a knife to scrape along the top to remove the extra flour.

Step 2: In a medium bowl, add the oil, lemon juice, eggs, lemon zest, vanilla extract, and non-dairy milk. Whisk the wet ingredients.

A photo of the wet and dry ingredients in a large mixing bowl.

Step 3: Pour the wet ingredients into the dry ingredients. For best results, mix them together until they are just barely mixed.

I like to let my batter sit for 15 minutes, but this is optional. For grittier gluten-free flour blends, this can help the cupcake texture by softening the rice flour in the blend.

🔑 Sandi says: The air bubbles from gently mixing your batter by hand help to make your cupcakes fluffy. Overmixing the batter will eliminate these air bubbles, leaving denser cupcakes.

Cupcake batter in a muffin tin ready to bake.

Step 4: Use a large cookie scoop or spoon the cupcake batter into a parchment paper-lined muffin tin to bake.

Fill each cup about 3/4 full of the gluten free cupcake batter so they can rise up but not spill over the top of the liner onto the muffin tin. This will also give you an even surface on top if you are going to frost the cupcakes.

Step 5: Bake at 350º F for 20-25 minutes until done. You can test to see if they are finished baking by inserting a toothpick in the center of a cupcake. If the toothpick comes out clean, the cupcakes are finished baking. If you see crumbs or batter, they will need to baked a little longer.

Step 6: Remove the cupcakes from the oven and allow your cupcakes to cool on a wire rack.

Now is a good time to mix the icing or frosting.

Ascooper that takes out the middle of the cupcakes.

Do not frost the cupcakes until they are completely cooled. You can use this contraption to scoop out some of the middles and fill the cupcakes with lemon curd if you prefer an even more lemony flavor!

TIP: If you want your frosting to be more lemon colored, add a few drops of lemon food coloring to the frosting as it mixes in your standing mixer. Here is an excellent guide to gluten free frosting, including how to color it.

A spoon drizzling icing over a cupcake.
This is what the older photo looked like from the original date in 2017.

These gluten free lemon cupcakes have a wonderful lemonade icing drizzle, making them so refreshing. For an extra fancy occasion, top them with your favorite frosting. Dig in!!

Cupcake Troubleshooting:

There are many reasons why your gluten-free cupcakes don’t turn out as expected. Here are the most common issues I hear from my readers and how to fix them!

Why are the cupcakes too moist?

If your cupcakes are too moist, you either didn’t bake them long enough, used too much butter or oil, or you used too much liquid. Every gluten-free flour blend has a different starch-to-grain ratio, and this affects the liquid levels as well as how the fat is absorbed in the flour blend. (Imagine starch and oil combined…it can make a pasty gunk. Many gluten free flour blends have a very high starch content.) If you use a flour blend different from the one I tested, be sure to look at my step-by-step photos and compare the batter consistency of your batter to mine.

Why did my cupcakes sink in the middle?

The two main reasons cupcakes sink in the middle are that you opened the oven door during the baking process or that you used too much liquid in the batter. I know you are tempted to open the oven door to get a better look at the cupcakes, but opening the oven door adds a blast of cool air, which can cause your cupcakes to fall.

Why did the cupcakes stick to the cupcake papers?

This is very common in gluten-free baking. I always recommend using parchment paper cupcake liners. It makes a huge difference! Using the right tools will always make a difference in baking.

For more help troubleshooting cupcake issues, read my Gluten-Free Cake Troubleshooting Guide. It is applicable to cupcakes as well! You can also learn a lot from my Gluten-Free Muffin Troubleshooting Guide.

Frequently Asked Questions

What makes a cupcake light and fluffy?

The best way to keep your cupcakes light and fluffy is to be careful not to over-mix the batter.

How do you store gluten free lemon cupcakes?

These cupcakes will keep fresh for up to 4 days in an airtight container. They also freeze really well and can be stored in the freezer for up to 4 months. I place cooled cupcakes in a freezer-safe zip-style bag.

Four lemon cupcakes on a wire rack.

Check out all of these incredible Gluten Free Lemon Desserts!

More Gluten Free Lemon Dessert Recipes:

Reader Reviews:

“So yummy! Love this recipe”

Lauren T, Pinterest User

Love This Recipe?

If you made and enjoyed this recipe, I would be incredibly grateful if you could leave a comment below. Please include which flour blend you used. This will help others know this recipe is delicious. Thank you!

Three lemon cupcakes on a plate. They are frosted and topped with lemon sprinkles.

Gluten Free Lemon Cupcakes with Lemonade Icing

Sandi Gaertner
Easy light and fluffy gluten free lemon cupcakes with a lemonade icing.
4.78 from 27 votes
dairy free allergen icon
gluten free allergy icon
nut free allergen icon
soy free allergy icon
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Gluten Free Cake Recipes, Gluten Free Dessert Recipes
Cuisine American
Servings 12 people
Calories 256 kcal


  • 2 ¼ cup gluten free flour blend * see note
  • 1 teaspoon baking soda
  • 1 ¼ cup sugar
  • 3 large eggs
  • 1 teaspoon pure vanilla extract
  • ¼ cup lemon juice
  • 1 tablespoon lemon zest
  • 1 ¼ cups almond milk * see note
  • ¼ cup coconut oil melted


  • 3 cups powdered sugar
  • 2 tablespoons lemon juice
  • 1 tablespoon lemon zest to top cupcakes with
  • ½ cup unsalted butter Softened, use dairy-free butter if you are dairy-free
  • Optional: 3-5 drops of yellow food coloring


  • Preheat the oven to 350º F. Be sure that the oven rack is in the middle setting.
  • Line a cupcake tin with paper cupcake liners. I like to use parchment paper liners so the cupakes don't stick to the paper.
  • In a large bowl, add all of the dry ingredients.
  • Whisk to blend these ingredients.
  • In a medium bowl, add all of the wet ingredients and whisk to blend them all together.
  • Pour the wet ingredients into the dry ingredients and mix until they are just barely mixed. This will help to keep your cupcakes light and fluffy.
  • Use a large cookie scoop to add the batter to each cupcake liner. Fill each cup about 3/4 full. Try not to overfill the batter or your cupcakes can rise too high.
  • Sprinkle the top of each cupcake with lemon zest.
  • Bake for 20-25 minutes until done. (*See note to test if they are fully baked)
  • Allow the cupcakes to cool on a wire cooling rack.
  • Mix all of the frosting ingredients in a stand mixer. Use the whisk attachment to make this frosting really fluffy.


  1. I have tested this recipe with two gluten free flour blends. King Arthur Measure for Measure GF Blend and Bob’s Red Mill 1 to 1 GF Blend. This does not mean they are the only two that work for this recipe. It just means I haven’t tested all of the gluten free flour blends out there.
  2. If your gluten free flour blend doesn’t contain Xanthan Gum, please add 1 teaspoon to the dry ingredients. For gum-free, use my DIY Gluten Free Flour Blend.
  3. Mix your cupcake batter for light and fluffy cupcakes until it is barely mixed; it will help make your cupcakes lighter and fluffier.
  4. To test to see if your cupcakes are done baking, insert a toothpick into a cupcake. if the toothpick comes out clean, your cupcakes are finished baking. If you see batter or crumbs, you will need to bake them a little longer.
  5. You can top these cupcakes with the icing in the recipe or frost them with buttercream frosting.
  6. These cupcakes will keep fresh for up to 3 days in an air-tight container in the refrigerator. You can also freeze them in a freezer bag for up to 4  months.


Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, you may need to adjust your moisture levels in your baked goods.


Serving: 1gCalories: 256kcalCarbohydrates: 48gProtein: 4gFat: 7gSaturated Fat: 4gCholesterol: 41mgSodium: 51mgPotassium: 86mgFiber: 2gSugar: 32gVitamin A: 59IUVitamin C: 2mgCalcium: 81mgIron: 1mg
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Nutrition Disclaimer

Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.

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