By Wendy Stoltz / Last Modified On January 15, 2023
You are going to love these simple, from scratch, Gluten-Free Lemon Cupcakes. This bakery-style cupcake is tender and has the perfect amount of lemon.
If you are looking for more gluten free cupcake recipes you might like my gluten free chocolate cupcakes. For more desserts check out my Gluten Free Desserts Recipes.
Gluten Free Lemon Cupcakes
These gluten-free lemon cupcakes are wonderful and will melt in your mouth. They are topped with a fluffy lemon butter cream frosting, adding just the right amount of tang for anyone who loves lemon desserts.
I originally posted this gluten-free cupcake recipe in April of 2014. My photography has improved by leaps and bounds over the past years, and I am having so much fun redoing photos for my recipes. I really want the photos to show you how wonderful these Gluten-Free Lemon Cupcakes are.
When I originally posted this recipe, I only took one photo. Over the years I've learned that people eat with their eyes, meaning the more photos the better! Within reason, of course.
Have you ever been to site that has ten to fifteen photos on each page? That's a bit too much for even me. I like to have three or four different shots of the recipe, showing different angles. And because that's what I like, I tend to now include three or four photos of the recipe in the post. If you don't want to see my lovely photos, simply scroll down.
These gluten-free lemon cupcakes are one of my all-time favorite gluten-free cupcake recipes. They are simple, fresh, and I just love the burst of lemon flavor you get with them.
Is lemon juice and lemon extract the same?
It's not the same. Lemon juice is acidic and can't be replaced with extract which is usually alcohol based. Similarly, fresh lemon juice and bottled juice react differently. In many cases bottled lemon juice causes batter to get rubbery. If a recipe calls for fresh lemon juice, use fresh lemon juice or you risk ruining the batter.
Gluten-Free Lemon Cupcakes
These Gluten-Free Lemon Cupcakes are MAGICAL! They have just the right amount of lemon that leaves you with a sweet and tangy finish and the frosting is second to none. Every time I bring these cupcakes to a party or a BBQ people tell me how refreshing they are.
Kids fight over them. Adults dive for them as soon as the plate hits the counter. I am lucky my family even lets me take them out of the house. Maybe it's because lemon is such a happy flavor, or maybe it's because lemons are yellow and yellow is a bright color, but lemon anything is a favorite of mine.
Just in case you were wondering, these cupcakes are neighbor tested and approved.
How to make gluten-free lemon cupcakes
There are a couple of tips and tricks to getting the right texture with gluten-free cupcakes. First, you have to follow the recipe. So many people comment on recipe posts saying that they made a ton of substitutions and the recipe didn't turn out. Other than the dairy substitute, I haven't tried other substitutes in this recipe. If you use substitutions, you are doing so at your own risk.
Second, you want to mix at the right time and not over-mix. When you are beating the oil, sugar, and eggs you'll want to beat it for the time listed. This adds air which in turn helps the cupcakes rise. Once you add your flour mixture, you'll only want to beat until combined. Beating any longer will cause the batter to stiffen.
Why did my gluten-free lemon cupcakes explode?
First off, you may have overfilled the cupcake wells. Never fill more then ¾ of the way full, and it's best to stick to around ⅔'s of the way full. I use a ¼ measuring cup to fill mine. Another reason could be that you added too much leavening agent, or that you are at higher elevation. Baking powder tends to work twice as hard at higher elevations. Consider cutting your baking powder in half if you are at a higher elevation.
These tips are relevant to most cupcake recipes, not just these Gluten-Free Lemon Cupcakes.
Working with Gluten-Free Flours
When working with or measuring gluten-free flour, spoon the flour into the measuring cup and level. Do not scoop your measuring cup into the gluten-free flour. The best method really is to weigh the gluten-free flour it but I don't have the ingredient weights for all my recipes yet.
What other milk can I use?
For this recipe I used almond milk, which is a dairy-free milk. You can use regular milk or you milk of choice.
If you like these gluten-free lemon cupcakes you might also like my Gluten-Free Vanilla Cupcakes. If you make this recipe please stop back by and let me know what you thought.
Did you make these gluten free lemon cupcakes? Please stop back by and let me know what you thought in the comments below.
Gluten-Free Lemon Cupcakes
You are going to love these simple, from scratch, Gluten-Free Lemon Cupcakes.
For the cupcakes:
- 1 ¼ cups gluten-free flour (I used Bob's Red Mill 1-to-1 gluten-free flour)
- 1 ½ teaspoons gluten-free baking powder
- ¼ teaspoon salt
- ½ cup oil
- ¾ cup sugar
- 2 large eggs
- 1 tablespoon gluten-free vanilla extract
- ¼ cup fresh lemon juice (from 1 medium lemon, not lemon juice from a bottle)
- 1 tablespoon lemon zest (from the same lemon)
- ½ cup milk (or dairy-free milk)
For the frosting:
- ½ cup butter (1 stick), room temperature (or dairy-free butter)
- 4 cups powdered sugar
- 2 tablespoons of lemon juice (or 1 teaspoon lemon extract)
- 3-4 tablespoons milk (or dairy-free milk), as needed
- For the cupcakes: Preheat oven to 350°F (180°C). Line a 12-serving cupcake pan with paper liners; set aside.
- In a medium mixing bowl, whisk flour, baking powder, and salt; set aside.
- In a large mixing bowl, with an electric beater, beat oil and sugar for one minute. Add eggs one at a time, beating in between each egg. Stir in vanilla extract, lemon juice, and lemon zest.
- Add the flour mixture and milk to the wet ingredients and mix just till combined. Don’t over mix!
- Divide batter among liners, filling ⅔ full (about ¼ cup of batter per cupcake).
- Bake for 18-20 minutes until a toothpick comes out clean.
- Cool completely before frosting.
- For the frosting: Beat butter until creamy. Add lemon juice or extract and beat till combined. Beat in 1 cup of powdered sugar at a time until it’s all added, alternating with 1 tablespoon of milk. Add more or less milk for desired consistency.
- Store cupcakes in an airtight container at room temperature for up to four days.
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Serving Size:1 cupcake
Amount Per Serving: Calories: 416Total Fat: 18gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 11gCholesterol: 53mgSodium: 188mgCarbohydrates: 61gFiber: 1gSugar: 49gProtein: 3g
I plan to make these cupcakes tomorrow. I have been baking GF for a few months trying out different recipes and love lemon. I have two questions. I have non-stick cupcake pans and wondered if I still needed to use the paper cupcake wrappers? Also, most recipes say to leave in pan 5 minutes before removing them to a rack. Do I put the item on the top of the hot stove (so it continues to cook) as I would with non-GF? Thank you.
You should be able to use your non-stick pan without papers. Watch the cooking time as the direct contact may bake them quicker. Since you are making them directly in the pan (no papers), I'd let them cook for 10 minutes, then run a soft rubber spatula around the edges before you transfer them to a cooling rack on the counter. You can leave the pan on the stovetop while they cool, before you transfer them.
Can you still make these without lemon zest?
Yes, you can.
Help! My cupcakes were a flop. I used the same flour and followed directions exactly but the cupcakes were spongy, rose then fell and stuck to the paper terribly. I had to throw them out. The batter seemed awfully runny and I wondered if the 1 1/4 cup of flour was correct. Any idea on what happened? I want to try your champagne cupcakes but don't want to make the same mistake.
When you say you used the same flour, what brand and bag color did you use? Also, are you at a higher elevation?
Hi I’m going to make these in two weeks and was wondering if the eggs/milk or any other ingredients should be at room temperature or if everything should be straight from the fridge? I didn’t see any notes on this! Thanks! 🙂
It's best to start with room temp ingredients, but you can use eggs and milk that are cold.
Update : just made them and they were done and perfect at exactly ten minutes.
We made these cupcakes with vanilla frosting and filled them with homemade strawberry syrup. We called them strawberry lemonade cupcakes and they were devoured!
Yes if you want them to be adorable and never trust nonstick pans they never work.
Hi, I apologize if I have overlooked it, but what kind of oil? Vegetable? The ingredient list doesn't specify. Thank you!
We like to use vegetable oil or avocado oil. You can also use melted and cooled coconut oil.
Hi Chrystal.. I just tried these.. I used coconut oil, and i used coconut sugar.. the cupcakes turned out very rubbery? not cake texture at all.. where did I go wrong? Please help.
I haven't used both coconut sugar and coconut oil in this recipe, it could have been that. What flour blend did you use?
I posted that I had trouble on September 2 with this recipe and you asked what flour I used and it was Bob's Red Mill 1 to 1. I'm not at a higher elevation. Do you think I didn't beat it long enough? I've been baking gluten free for many years but am learning how to use these 1 to 1 flours.
You don't need to mix that batter for too long, but you do need to mix it long enough to add air bubbles. Also, for the lemon cupcakes, it's important to use fresh lemon juice, not bottled, as the bottled juice has a different acidic structure.
I hope that helps.
Can you use coconut sugar instead?
Another reader used coconut sugar and coconut oil and they came out rubbery. I am not sure as i have not tested it myself. Let us know if you do.
These look beautiful and delicious!! I'm on cupcake duty for a baby shower in about a month, and the couple is gluten free so I'm planning to use this recipe. However, I'm vegan so I don't buy eggs - do you have any tips or recommendations for how to make these also egg-free? I'll probably test this recipe out once or twice before the actual baby shower, so I can give an update on which egg replacements I used and how they turned out. Just wondering if you recommend any starting points!
You can start with using chia egg and whip them with an electric mixer to add a little air. You might also try aquafaba. Just note, I haven't tried these in this recipe. I do have a vegan chocolate cupcake recipe, if you want to try that.
Love these lemon cupcakes! My daughter and her fiancé are getting married this fall and will be having a traditional wedding cake, but I have been told I must make these for the celiac folks which includes myself, my twin sister, the maid of honour and best man! I've already experimented by freezing them fully iced, then taking them out to thaw in the refrigerator and they taste perfectly fresh. They're so good I might have to make a bit extra for the people who are going to be jealous watching us enjoy them! (BTW, I've tried many of your recipes and you are by far the best gluten free baking blogger I've found. I haven't had a failure yet!) Thank you!
You are very welcome! I a so glad you like them. Congrats to your daughter and her fiancé!
Perhaps this is a silly question, but are these standard or mini cupcakes? Just looking at the ingredient list, I wonder about the volume to make 12 cupcakes ♀️
This makes 12 standard sized cupcakes.
These are the best cupcakes I have had! They beat any gluten cupcake I have had. Thank you for the recipe! I will.be making these again for sure!!!
I am so glad you like them. Thank you for letting me know.
I have also used grapeseeed oil and they turned out amazing.
Do you have any tips for mixing by hand? Ex. whisk or fork, consistency, etc. I don't have an electric mixer unfortunately.
If you mix by hand, use a whisk.
will this recipe work also if I want to make a cake and use a cake pan?
I haven't personally tried this recipe as a cake but I do have a separate recipe for lemon cake, that's a little different from this one.
Can I use your gf flour blend #1 and add xanthum gum to make these cupcakes? I always prefer to use my homemade flour blends. Also can I use vegan margarine or shortening for the icing. I have to make them dairy free & gluten free.
Yes, you can use my flour blend #1 and add xanthan. Vegan butter or margarine will work for the frosting, but it may be a softer.
Hi, I was wondering if I want to make the frosting with cream cheese as well, would you recommend 1/4 cup butter & 1/4 cup of cream cheese?
You can use half butter and half cream cheese. I haven't tried lemon juice with cream cheese myself but lemon extract works well with cream cheese frosting and buttercream frosting.
I want to make half a dozen (6) cupcakes. Can I half the ingredient quantities?
Yes, I recommend writing it out as half, that way there isn't anything accidently added as the full amount.
I made them with your gluten free flour blend & xanthum gum. They were delicious! I will make these cupcakes often.
Would these work with the white rice flour blend from what the fork blog? I made these before with namaste flour and they were terrible. (Blaming the flour blend, your recipe looks amazing!)
Sharon has two blend that use rice flour. If it's her all purpose with rice, tapioca and potato starch, yes it will work, it's similar to my blend. I definitely don't recommend the Namaste flour blend in any of my recipes, it doesn't taste the same and it doesn't yield good results.
Hi there! I regularly make your Vanilla GF cupcakes (they're our absolute family favourite!), and they come out perfectly every time. I made these today for the first time, but a) I wasn't sure how long to mix after the additional of each egg, and b) when I added my dry to my wet the mixture was very lumpy, so I needed to mix more than I think I should have. They rose very well but then fell (still domed, just considerable sinking as they cooled!), and have a doughy texture I've never had with the vanilla ones. Was it overmixing that likely caused this? The other thing is that for your vanilla ones I use Dove's Plain Flour (no xantham in the blend) and add 1/4t of xantham gum and get perfect results. I did the same here - would it react with the acidity of the lemon in some unfavourable way? Other than the lemon zest and juice the recipes look very similar? Any help would be much appreciated!
It could have been that it was overmixed. You just want to mix this batter until it's combined. Also, I haven't personally used the Dove's flour mix, which has slightly different ingredients in it. Next time, mix just until combined (although there shouldn't be lumps) and then baked a couple minutes longer to see if that helps.
You have oil in the ingredients. Most cakes use vegetable oil. Am I supposed to use vegetable oil?
Yes, vegetable oil works best in this recipe.
I make a yummy lemon cake (not gluten free) and add white chocolate chips which everyone loves.
I have a few friends who are GF and I would like to make these cupcakes for them.
Can I add some white chocolate chips to this recipe?
I haven't personally added chocolate chips, but it should work fine.
Which milk other than almond milk is good to substitute with?
You should be able to use any type of milk that you enjoy drinking. Almond, soy, oatmilk, or coconut milk will work. Thanks for stopping by!
Not great. I used cashew milk and canola oil. Not impressed at all. Gummy gooey texture. Gross earthy flavor. Such a waste. Don't use cashew milk, maybe don't use canola.
Hi Rachel, Thanks for stopping back and letting us know your experience. The ingredients you use can definitely affect the final outcome - it can sometimes take some trial and error to make substitutions with GF recipes. Read though the post and comments if you decide to try again, there are some great tips!
Minister of Recreation
I used coconut oil and the cupcakes were perfectly textured and so tasty. Thank you!
We are so glad you enjoyed them!
Do you have a preferred oil you use for this recipe?
Hi Tiffany, vegetable oil or canola oil is what I typically use. Enjoy!
I made these and followed all directions. My question is do you have an idea of why these might separate from the liners? BTW I made your red velvet and everyone thought they were wonderful!!
Sometimes if that happens it can mean that they are a bit overcooked. if the cupcakes are dry they can shrink and separate from the liners. Maybe reduce the cook time by a few minutes next time.
Hi I’m 10 and I made these by myself. Super yum except only made 6.
Hi Chloe! That is so cool! I'm very impressed with you 🙂
Can you add blueberries to this recipe? If so, how much do you think to add?
Hi Karen! Yes, you'd be making sort of a mashup of this cupcake recipe and our gluten free blueberry cupcakes. I'd add 1 cup of fresh berries to this lemon cupcake recipe, or try the blueberry cupcakes and add lemon extract and lemon zest to the batter.
Should a regular grocery store have GF baking powder and GF baking soda? I've never noticed it. Would the outcome be bad if I didn't use GF ?Thank you!
Hi Candyce! If you are needing to avoid gluten, you should just check to be sure that all of your ingredients are gluten-free. Not all brands of these products are safe for people with celiac disease due to added ingredients or cross-contamination concerns. Arm and Hammer baking soda is gluten free, as is Clabber Girl baking soda.
I see milk as an ingredient in the batter but don’t see where to add it? Does it go in with the wet or is it a typo to have it as an ingredient in the batter?
Hi Elieen, View step 4, the milk is added then.
I made these cupcakes for my 18 year old's birthday celebration. One of the boys who came had brought his own GF brownie because he is gluten free and normally can't eat the dessert at any parties. His eyes lit up and he asked if he could have one when I said the cupcakes were gluten free. My son used not to like GF food, but he and all his friends loved these cupcakes. They had just the right amount of lemon and were super moist. I'm glad I doubled the recipe to have twice the number of cupcakes! Thanks for a great recipe!
Hi Nancy, oh wow, that is so special for the boy! Happy birthday to your child!
I followed this recipe to the letter except I only had the regular Red Bag of Bob's GF flour on hand (not the1:1). I used regular milk and fresh lemon juice. Turned out excellent! I was worried that the batter was a little thin but no worries at 20 minutes in the oven. Tip: Read all the great tips on this page before baking this (measuring, beating, gently mixing etc.) and if you're worried about the muffins sticking to the paper just very, very lightly spray the liners with Pam before adding the batter. These are freaking delicious and I will definitely double this recipe next time. Thank you for a great GF recipe!
Thanks Rhonda, so pleased you enjoyed it. Thanks for reading all the tips!
These cupcakes are amazing. Will definitely make these again.
Thank you Rose, appreciate your feedback!
Hi, I made these with Bob's Red Mill 1:1 flour and they turned out spectacularly. I used avocado oil, superfine sugar and sicilian lemon juice (from a bottle - nice and tart). The tops are a bit caramalized and the inside so light and fluffy! In reading some people's comments, I wonder if they used Bob's All Purpose flour (which has bean flour in it) and not Bob's 1:1??? I had some home-made lemon curd to use up so I took a little core out of each cupcake and added 1 tsp. lemon curd to the centre of each cupcake before icing. Yum!I did follow your instructions to the letter and I am very, very happy with the results!
Thanks, Jilian. So pleased you enjoyed the recipe!