• Bloglovin
  • Facebook
  • Instagram
  • Pinterest
  • RSS
  • Twitter
  • Recipe Index
  • About
  • Work with Me
  • Portfolio
  • Contact
  • FAQ
  • Skip to primary navigation
  • Skip to main content
  • Skip to primary sidebar
  • Skip to footer

Snixy Kitchen

A Bay Area gluten-free food blog with original seasonal recipes

  • RECIPE INDEX
  • Season
    • Spring
    • Summer
    • Fall
    • Winter
  • Gluten-Free
    • Gluten-Free Desserts
    • Gluten-Free Savory
  • Breakfast
  • Appetizers
  • Dinner
  • Desserts

Gluten-Free Lemon Cupcakes with Lemon Cream Cheese Frosting

April 26, 2019 by Sarah Menanix

Jump to Recipe
  • Share
  • Tweet

Last updated on January 19th, 2021

Gluten-Free Lemon Cupcakes with Cream Cheese Frosting

These light and fluffy gluten-free lemon cupcakes topped with lemon cream cheese frosting burst with lemon flavor. This easy recipe has a moist crumb and will be the highlight of any party!

Gluten-Free Lemon Cupcakes with Cream Cheese Frosting

Gluten-Free Lemon Cupcakes with Cream Cheese Frosting

These aren’t just any gluten-free lemon cupcakes. They’re the lemon cupcakes we served at our wedding. The same lemon cake recipe we used to make our mini cut cake (you know, the one we tried to eat out of the freezer on our first anniversary). These cupcakes are special.

Back when we got married – almost six years ago – I’d just started experimenting with cutting gluten out of my diet. I dramatically swore off gluten about a month and a half before the wedding. But what about the cake?!

Gluten-Free Cupcake Recipe

Gluten-Free Lemon Cake with Cream Cheese Frosting

My friend who’d just finished pastry school had agreed to make the cupcakes for our wedding. After spending a day several months before the wedding recipe testing cupcakes in her kitchen, we landed on the perfect lemon cupcake recipe. I think she also made pumpkin spice and red velvet cupcakes for the big day, but they clearly didn’t leave an imprint like the lemon cupcake. Just because I’d broken up with gluten, I wasn’t about to skip out on those lemon cupcakes. So she made the lemon cupcakes with a bag of all-purpose gluten-free flour. 

Now that I’m six years into baking gluten-free (with lots of tips and tricks shared by my friend Alanna), I can finally do these cupcakes more justice as a true made-from-scratch gluten-free lemon cupcake.

Also, I just re-read that diatribe against gluten and I’m still baking my way through the 1000 cupcake liners I ordered for our wedding…six years later. And not for lack of trying – I bake a lot of gluten-free cupcakes. 

Gluten-Free Lemon Cupcakes with Cream Cheese Frosting

Lemon Frosting for Cupcakes

How to make gluten-free lemon cake

This gluten-free lemon cake recipe starts with a vanilla cake base. Reduce the vanilla and add lemon zest and lemon juice.

To make the cake gluten-free, I use a trio of gluten-free flours: oat, millet, and sweet rice. These flours blend together to behave much like an all-purpose flour in baked goods like cake. While you get a bit of warm whole grain notes, their flavors are subtle, which allows the lemon to shine. 

If you’re hesitant to buy three bags of gluten-free flour, check out my recipe page to filter recipes by flour to use up every last ounce.

Do I need xanthan gum for Gluten-Free Cake?

No. And yes. Ha – you like that?

NO, you don’t need xanthan gum in gluten-free cake. If your flour blend uses a high ratio of sweet rice flour, it acts much like xanthan, giving the cake the sticking power that lends to a beautifully chewy crumb. So if you can’t or choose not to eat xanthan gum, you can rest assured that leaving it out of any cake recipe on my site won’t ruin your cake!

But YES, you may want xanthan gum in your gluten-free cake. This gluten-free cake recipe calls for xanthan gum as optional. Cupcakes with xanthan gum will be a little fluffier and less dense, and will have a springy chew more like regular cupcakes. I prefer that.

If you’re just starting out with gluten-free baking, the hefty price tag on xanthan gum is enough to steer folks away from using their own flour blends that require it. That being said, I keep it in my fridge and a bag lasts me almost 2 years, so if you plan on getting more serious about gluten-free baking, a little goes a long way. 

Gluten-Free Lemon Cupcakes Recipe

Lemon Gluten-Free Cupcakes

How to convert cupcakes into a gluten-free lemon cake?

If you want to make these gluten-free lemon cupcakes as a lemon cake instead, use this conversion:

12 cupcakes = one 8-inch cake

24 cupcakes = three 6-inch cakes

24 cupcakes = one 9×13 cake

You’ll need to adjust the baking time for the cakes. Your cake is done when a finger lightly tapped in the center springs back and doesn’t leave an imprint. A toothpick inserted into the center should come out clean or with a few crumbs. I usually only set a timer to remind me I have cake in the oven, but bake based on the visual cues. 

Here’s how I’d set my timer for the above cakes: The 8-inch cake will take about 33-37 minutes, the 6-inch cakes will be thinner, so start checking for doneness around 25 minutes, and the 9×13 cake will take 40-50 minutes. 

Lemon Cupcakes with Cream Cheese Frosting: How to make lemon frosting for cupcakes

The tanginess of lemon cream cheese frosting is the perfect complement for a sweet and tart lemon cupcake.

Adding lemon juice to the frosting can make it soft and hard to pipe. Instead, infuse lemon into the cream cheese frosting by adding plenty of lemon zest.

Here’s the closed star pastry tip I use for my cupcakes. To get bakery-style frosting, start piping in the center of the cupcake working outwards, then doubling up when you get to the edge and coming back to the center. 

Gluten-Free Cupcake Recipe with Lemon

Got a bunch of lemons? Bake a batch of gluten-free lemon cookies too!

More Gluten-Free Cupcake Recipes

Here are a few of my favorite gluten-free cake recipes. Get all my gluten-free cake recipes in my recipe index.

Gluten-Free Chocolate Cupcakes

Gluten-Free Vanilla Cupcakes

Earl Grey Gluten-Free Bundt Cake

Gluten-Free Vanilla Raspberry Sheet Cake

Continue to Content
Gluten-Free Lemon Cupcakes with Cream Cheese Frosting

Gluten-Free Lemon Cupcakes with Lemon Cream Cheese Frosting

Yield: 12 cupcakes
Prep Time: 12 minutes
Cook Time: 24 minutes
Additional Time: 10 minutes
Total Time: 46 minutes

These light and fluffy gluten-free lemon cupcakes topped with lemon cream cheese frosting burst with lemon flavor. This easy recipe has a moist crumb and will be the highlight of any party!

Ingredients

Gluten-Free Lemon Cupcakes

  • ½ cup (81g) sweet rice flour or glutinous rice flour (such as Mochiko - different from "white rice flour" or "brown rice flour")
  • ½ cup + 2 tablespoons (75g) gluten-free oat flour*
  • ½ cup (78g) millet flour
  • ½ teaspoon xanthan gum (optional**)
  • 1½ teaspoons baking powder
  • ½ teaspoon kosher salt
  • ½ cup unsalted butter, room temperature
  • 1 cup (208g) granulated sugar
  • 2 large eggs, room temperature
  • 3 tablespoons fresh lemon juice (From 2-3 lemons)
  • 2 tablespoons lemon zest (3-4 lemons)
  • 1 teaspoon pure vanilla extract
  • ½ cup whole milk or buttermilk***

Lemon Cream Cheese Frosting

  • 8oz cream cheese, room temperature
  • 1/2 cup (4oz) butter, softened
  • 1½ cups powdered sugar, sifted
  • 1½ tablespoons lemon zest (from about 3 lemons)
  • ½ teaspoon pure vanilla extract
  • Pinch of kosher salt

Instructions

Gluten-Free Lemon Cupcakes

  1. Preheat the oven to 350°F.
  2. In a medium bowl, sift together the sweet rice flour, oat flour, millet flour, xanthan gum (if using), baking powder and salt. Set aside.
  3. In the bowl of a stand mixer, cream together the butter and sugar over medium speed until light and fluffy, about 3 minutes.
  4. With the mixer on low-speed, add the eggs one at a time, mixing after each one.
  5. Add the lemon juice, lemon zest, and vanilla extract, mixing until just combined.
  6. Keeping the speed on low, slowly add the dry ingredients in two batches, adding the milk in between, mixing until just combined.
  7. Divide the batter among 12 lined cupcake cups, until about 1/2 to 2/3 full.
  8. Bake for about 22-26 minutes, or until the tops bounce back a little when tapped and a toothpick inserted in the center comes out clean or with just a few moist crumbs.
  9. Transfer the cupcakes to a wire rack to cool completely before frosting
  10. Prepare the frosting.

Lemon Cream Cheese Frosting

  1. In the bowl of a stand mixer fitted with the paddle attachment, cream the butter over medium speed.
  2. Add the cream cheese and beat until completely smooth.
  3. Slowly add the powdered sugar, in thirds, mixing on low speed until combined.
  4. Add the lemon zest, vanilla and salt, and beat on medium speed until smooth.
  5. Pipe or spread onto cooled cupcakes. For the pattern above, use a large closed-star pastry tip.

Notes

*I use homemade oat flour by grinding gluten-free rolled oats in my blender or food processor until fine.There is a small difference in cupcakes baked with store-bought gluten-free oat flour versus those baked with home-ground gluten-free oat flour, where the store-bought oat flour cupcakes rose just ever so slightly less, but still made a delicious cupcake.

**You can leave out the xanthan gum if needed, but the result is a slightly gummier more dense cupcake.

***You can use either milk or buttermilk and they'll both produce a delicious cupcake. I use whole milk usually because I always have it on hand, but if you happen to have some leftover buttermilk on hand, sub that in to enhance the tangy notes.


© Sarah Menanix
Category: Cakes & Cupcakes
  • Share
  • Tweet
instagramIf you make this recipe, tag your photo #SnixyKitchen on Instagram!

Cakes & Cupcakes, Desserts, Flour, Fruit, Gluten Free Desserts, Gluten-Free, Meal Type, Millet Flour, Oat Flour, Season, Special Diet, Spring, Summer, Sweet Rice Flour

Snixy Kitchen

SUBSCRIBE NOW

get free recipes straight to your inbox:

Previous Post: « Soft Lofthouse Style Gluten-Free Sugar Cookies
Next Post: Gluten-Free Almond Flour Pasta »

Reader Interactions

You may also enjoy:

Soft and Chewy Gluten-Free Lemon Cookies
Chewy Gluten-Free Lemon Cookies
Gluten-Free Coffee Cake
Gluten-Free Coffee Cake
Gluten-Free Birthday Cake Recipe
Gluten-Free Vanilla Cake
Gluten-Free Pumpkin Roll
Gluten-Free Pumpkin Roll

8 Comments

  1. Iram -

    April 29, 2019 at 5:16 am

    I made these yesterday for my little girl with Celiac disease. The whole family liked them very much. Delicious and fluffy as promised.will. E making them again.

    Reply
  2. Marcella -

    November 24, 2019 at 2:04 pm

    Making this right now and I don’t see how much baking soda to add?

    Reply
    • Sarah Menanix -

      November 27, 2019 at 9:54 am

      I’m so sorry for the delay! Your comment when to my spam for some reason. That was a typo from when I’d copied over my instructions from my vanilla cupcake recipe – updated!

      Reply
      • Marcia Karls -

        October 3, 2020 at 1:34 pm

        Is it baking soda or powder?

        Reply
        • Sarah Menanix -

          October 3, 2020 at 1:52 pm

          Only baking powder! (In the instructions I had copied over it had originally mistakenly said “add the baking powder and baking soda” when it should have just said baking powder, hence the confusion. The recipe above is correct).

          Reply
  3. Ann -

    January 27, 2020 at 1:41 pm

    I don’t have millet flour, but I do have sorghum flour and buckwheat flour. My instinct is to substitute the millet flour with sorghum flour. How do you think that would work? I’d prefer not to buy yet another kind of flour (I have at least 5 types ????). Thanks for a recipe that looks like it’s going to make me very happy!

    Reply
    • Sarah Menanix -

      January 27, 2020 at 2:38 pm

      While I haven’t tried it in this recipe, sorghum flour would be the best bet here – substitute it by weight! I have other muffin recipes that I use sorghum in place of millet and it works great. It bakes up similarly to millet flour, but will have a slightly more sweet wholesome flavor. The color may also be a tad darker with sorghum flour. Best of luck!

      Reply
  4. Marie -

    April 22, 2020 at 2:18 pm

    What a treat! The texture is not crumbly but moist and tender and just the perfect amount of lemony goodness. I made my own oat flour and they were delicious. Will definitely make these again.

    Reply

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Primary Sidebar

Sarah Menanix

I’m Sarah (aka Snix)! Welcome to Snixy Kitchen - where I create gluten-free recipes with fresh, local ingredients to tell stories about my life.

More about me ➤

STAY IN TOUCH

get new recipes to your inbox:

The Ultimate Guide to Matcha

Popular Posts

Best Vegan Gluten-Free Chocolate Chip Cookies

Vegan Gluten-Free Chocolate Chip Cookies

Vegan Triple Berry Crumble with Cinnamon Breadcrumbs

Quick Stovetop Gluten-Free Berry Crisps

Gluten-Free Chocolate Ice Cream Cake

Chocolate Gluten-Free Ice Cream Cake with Caramel

Gluten-Free Cream Puffs

Gluten-Free Cream Puffs

Gluten-Free Breakfast Oatmeal Jam Bars

Gluten-Free Breakfast Oatmeal Jam Bars

Gluten-Free Snack Tahini Coconut Flour Cake with Chocolate Buttercream

Gluten-Free Tahini Snack Cake with Chocolate Buttercream

KitchenAid Stand Mixer

Footer

Chewy gluten-free lemon cookies with crisp edges. Chewy gluten-free lemon cookies with crisp edges. This cookie marks the shifting of micro-seasons from Holiday Winter to New Year Winter (TM). It's a subtle change, one mostly perceivable in the baked goods coming out of each, but one that I believe should be celebrated with plenty cookies (both before and after the seasonal shift). 
•
So here are are, firmly in the land of backyard citrus, so I’m making all the lemon desserts. These cookies have sturdy crisp edges with a soft and fluffy, but intensely chewy center and a punch of lemon. Get the recipe link in my profile @snixykitchen. 
•
#lemoncookies 
https://www.snixykitchen.com/chewy-gluten-free-lemon-cookies/
Time to dig into citrus season! Get the recipe for Time to dig into citrus season! Get the recipe for this gluten-free earl grey bundt cake with blood orange drizzle on the blog - link in profile @snixykitchen. 
•
Last year, Zoella (4) peeled and ate a blood orange she’d found in a bush in our side yard when we weren’t looking. We found the sticky peels on the steps and panicked - where did this blood orange come from? Did an animal bring it? Is she going to get sick?! 
•
And that’s how we discovered our neighbors have a blood orange tree. By that point, it had dropped most of its fruit except for a few very high up branches that leaned over our fence. The tree is fruiting and nearly ripe again so I’m hopeful I can barter for a bag of oranges in exchange for some slices of this bundt cake. 
•
#glutenfreecake #bundtcake #bloodorangecake

https://www.snixykitchen.com/earl-grey-gluten-free-bundt-cake-blood-orange-icing/
We’re mixing up our meal planning routine with t We’re mixing up our meal planning routine with this savory gluten-free dutch baby topped with gruyere, a pile of buttery thyme mushrooms, and garlic wilted Baby Kale. Getting out of our dinner rut feels refreshing! Made in partnership with @plenty, this breakfast, lunch, or dinner anytime dish shows off their pesticide-free greens that are vertically farmed right here in the Bay Area. I’ve told you this before and it’s not an exaggeration when I say these are my favorite greens – they somehow taste fresher and more vibrant. 
•
I dropped some of this dutch baby off with my neighbor and, without prompting, she immediately texted, “YOM. I would make this. Greens are hella good.” It’s true. The greens are the star. If you’re in the Bay Area, use the link in my profile to find out where to get them near you!
•
Related big news: Ira (2) voluntarily ate cooked Baby Kale without throwing it on the floor or sneakily moving it to his sister’s plate. Even Ira knows a good thing when he sees it. 
•
For the gluten-free dutch baby recipe, search “almond dutch baby” on snixykitchen.com. Omit the sugar, cinnamon, and vanilla, and top it with grated gruyere 5 minutes before it’s done. For topping, saute some mixed mushrooms in butter with fresh thyme, and sliced garlic. Then add a few handfuls of Baby Kale and toss just to wilt. Salt & pepper to your heart’s content. If you want the extra flare, add a runny fried egg (eggs on eggs – why not?).
•
Sponsored by Plenty #plentyforall, #greensdontsuck https://bit.ly/3kZqAql
The toughest choice of the season: which cookies t The toughest choice of the season: which cookies to make for Christmas?! How many kinds is too many for a family of four? These buttery melt-in-your-mouth gluten-free white chocolate matcha shortbread 🎄 are a high contender! A snappy crumb and a nutty matcha flavor thanks to my fav @myencha! 😽 Get the recipe link in my profile @snixykitchen 
•
What are your must-make holiday cookies this year??
•
https://www.snixykitchen.com/gluten-free-white-chocolate-matcha-shortbread-cookies/ #christmascookies #matcha #myencha #glutenfreecookies #shortbreadcookies
Ultra chewy gluten-free blondies. A cross between Ultra chewy gluten-free blondies. A cross between a cookie bar and a brownie, they’ve got a vanilla cookie-dough with rich toffee notes from browned butter and dark brown sugar. A crackly top with classic brownie crispy edges and chewy center. Made in partnership with @bobsredmill (ad), they’re infinitely customizable with your favorite add-ins! Head to my stories to learn about why I chose chocolate chips instead of chopped chocolate chunks. 
•
This final recipe uses almond flour, with an options for nut-free and grain-free versions. I tested multiple leading flours and, in a blind taste-test with 10 of my neighbors, every single one chose this almond flour version, describing it as “classic.” So there you go - get the recipe link for these classic chocolate chip blondies in my profile @snixykitchen.
•
https://www.snixykitchen.com/gluten-free-blondies/ #blondies #glutenfreerecipes #glutenfreecookies #glutenfreeblondies #betterwithbobs #bakedwithbobs
It’s about time for our annual sugar cookie sess It’s about time for our annual sugar cookie session. This is what my sugar cookies look like when I decorate them by myself without kids. The ones we make for Santa will surely be rainbow swirled and very messy with a pile of sprinkles as thick as the cookie (I’ve heard that’s how Santa likes them anyhow). Get my cut-out sugar cookie recipe link in my profile. 
•
Fun fact: I had to buy these holiday cookie cutters specifically for this post. There was a good couple of years where I only had a hippo cookie cutter and made holiday hippos every year. I still prefer my more eclectic cutters to the traditional ones. What’s your favorite cookie cutter in your collection?
•
https://www.snixykitchen.com/gluten-free-sugar-cookies-with-easy-icing/. #sugarcookies #glutenfreerecipes #glutenfreecookies #glutenfreesugarcookies
{New} This classic gluten-free coffee cake is fluf {New} This classic gluten-free coffee cake is fluffy and moist and everything I’ve been craving about a bakery-style coffee cake.
•
I don’t know about you, but I could use a warm hug right about now. A slice of coffee cake with a ribbon of cinnamon sugar, a pile of streusel, and a vanilla icing drizzle feels like the food equivalent to that. You’ll find me snuggled up under my favorite blanket with a cup of tea and a slice of coffee cake every evening this week. Find the recipe link in my bio @snixykitchen. 
•
#coffeecake #glutenfreecake https://www.snixykitchen.com/gluten-free-coffee-cake/
Chewy Gluten-Free Chocolate Cookies. Zoella begged Chewy Gluten-Free Chocolate Cookies. Zoella begged for a rainy day hot cocoa and cookies date, so we made hot cocoa and a batch of these deep dark gluten-free chocolate cookies. And the cookie-a-day holiday menu continues. To get the recipe, go to @snixykitchen and tap the link in my profile!
•
https://www.snixykitchen.com/chewy-gluten-free-chocolate-cookies/
Follow @snixykitchen on Instagram

SEARCH

  • Bloglovin
  • Facebook
  • Instagram
  • Pinterest
  • Twitter
  • Meet Sarah
  • Contact
  • FAQ
  • Recipes

ALL CONTENT & IMAGES Copyright © 2021 Snixy Kitchen
privacy policy | disclosure