If you’ve been searching for a burst of bright, zesty flavor in a tender, moist treat that’s also friendly to gluten-sensitive diets, this Gluten-Free Lime Agave Cupcakes Recipe is your new best friend. These cupcakes combine the refreshing zing of lime with the natural sweetness of agave syrup, all wrapped up in a light, fluffy texture thanks to thoughtful gluten-free ingredients. Perfect for celebrations or an everyday indulgence, they balance tangy and sweet with such ease that every bite feels like a mini party in your mouth.

Ingredients You’ll Need
Good recipes start with great ingredients, and this cupcake recipe relies on simple yet essential components that each play a vital role. From the gluten-free flour blend that forms the perfect base to the creamy Greek yogurt that adds moisture and richness, every item enhances the flavor, texture, or vibrant lime notes.
- 1½ cups gluten-free flour blend: Provides a sturdy yet tender cupcake foundation without gluten.
- ¼ cup arrowroot starch: Helps lighten the texture and keep the crumb soft.
- 1 teaspoon xanthan gum: Adds binding strength, mimicking gluten for that perfect chew.
- 1 teaspoon baking powder: Gives lift and airy softness to the cupcakes.
- ½ teaspoon baking soda: Helps balance acidity and encourages rise.
- ¼ teaspoon salt: Enhances all the sweet and tangy flavors without overpowering.
- 2 large eggs, room temperature: Key for structure and emulsification to create a smooth batter.
- ½ cup agave syrup: Natural sweetness that’s liquid and perfect for tender crumb.
- ¼ cup coconut oil, melted and cooled: Adds subtle richness and moistness with a tropical hint.
- ½ cup Greek yogurt: Boosts moisture and brings a mild tang that complements lime perfectly.
- ¼ cup buttermilk: Provides acidity to react with leaveners for height and softness.
- 1 tablespoon lime zest: Infuses fresh citrus oils and bright flavor.
- 2 tablespoons fresh lime juice: Builds that unmistakable lime punch.
- 4 ounces cream cheese, room temperature: For swirled pockets of creamy, tangy delight.
- 2 tablespoons agave syrup (for cream cheese swirl): Sweetens and smooths out the cream cheese.
- 1 teaspoon lime zest (for cream cheese swirl): Echoes the lime flavor in the swirl filling.
- 1 cup powdered sugar (for glaze): Creates a sweet, silky topping.
- 2 tablespoons fresh lime juice (for glaze): Lightens and flavors the glaze with authentic zest.
How to Make Gluten-Free Lime Agave Cupcakes Recipe
Step 1: Preheat and Prepare
Start by preheating your oven to 350°F and lining a 12-cup muffin tin with paper liners. Using eggs at room temperature makes a big difference, as they emulsify better, helping your cupcakes rise into perfectly tender shapes.
Step 2: Mix Dry Ingredients
Whisk together the gluten-free flour blend, arrowroot starch, xanthan gum, baking powder, baking soda, and salt in a large bowl. This ensures even distribution of leavening and helps create an all-around fluffy texture.
Step 3: Combine Wet Ingredients
In a separate bowl, beat the room temperature eggs with agave syrup until pale and slightly thickened. Gently stir in the melted coconut oil, Greek yogurt, buttermilk, lime zest, and lime juice. Mix just until everything comes together to keep the batter tender.
Step 4: Incorporate Wet and Dry
Pour the wet mixture into the dry ingredients and fold gently until no flour streaks remain. Be cautious not to overmix — this helps prevent a dense cupcake and keeps them light.
Step 5: Prepare Cream Cheese Swirl
Beat together cream cheese, agave syrup, and lime zest until smooth in a small bowl. This creamy swirl adds a luscious burst of tangy flavor in every bite.
Step 6: Layer Batter and Swirl
Spoon one tablespoon of batter into each muffin liner. Add a teaspoon of the cream cheese mixture on top, then cover with another tablespoon of batter. Use a skewer to gently swirl the cream cheese into the batter, creating beautiful marbled pockets without overmixing.
Step 7: Bake to Perfection
Bake for 18 to 22 minutes until edges are set and a toothpick comes out with a few moist crumbs. Avoid overbaking to keep them delightfully moist.
Step 8: Cool Properly
Let your cupcakes cool in the pan for 5 minutes before transferring to a wire rack. This helps them set well and prevents sogginess on the bottoms.
Step 9: Make the Lime Glaze
While cooling, whisk powdered sugar and lime juice until smooth and pourable. Adjust the consistency as needed to get the perfect drip glaze texture.
Step 10: Glaze and Finish
Once cupcakes are lukewarm, dip or drizzle the glaze on top, then let it set. This final step adds a shiny, tangy finish that makes these cupcakes truly irresistible.
How to Serve Gluten-Free Lime Agave Cupcakes Recipe

Garnishes
Adding a small mint leaf or an extra sprinkle of lime zest on top can elevate the presentation and enhance the fresh citrus aroma. Thin slices of lime or edible flowers also make charming, Instagram-worthy accents.
Side Dishes
Pair these cupcakes with a light lemon or lime sorbet, or a simple fresh fruit salad featuring berries and kiwi to complement the tangy flavors. A smooth cup of herbal tea such as chamomile or green tea balances the sweetness beautifully.
Creative Ways to Present
Try serving these cupcakes on a rustic wooden board with vibrant tropical leaves underneath for an inviting, festive look. You can also place each cupcake in colorful paper liners and stack them in a tiered cake stand for parties. For an interactive touch, offer a variety of glazes or toppings so guests can personalize their cupcakes.
Make Ahead and Storage
Storing Leftovers
Store your gluten-free lime agave cupcakes in an airtight container at room temperature for up to 2 days. If your home is warm, refrigeration can help preserve freshness but allow cupcakes to come to room temperature before eating to enjoy the best texture.
Freezing
These cupcakes freeze beautifully! Wrap each individually in plastic wrap and place in a freezer bag or container for up to 3 months. Thaw overnight in the fridge or at room temperature before glazing or serving.
Reheating
To warm up your cupcakes, pop them in the microwave for about 15 seconds or until just warm — avoid overheating as it can dry them out. Warm cupcakes bring out the lime aroma even more and soften the glaze for extra indulgence.
FAQs
Can I substitute agave syrup with honey?
Yes! Honey is a great substitute for agave syrup and will work similarly to sweeten your batter and swirl, but it may add a slightly different floral note. Just use the same quantity for best results.
What gluten-free flour blend works best?
A blend that contains rice flour, tapioca starch, and potato starch typically works well as it mimics the texture of all-purpose flour. Avoid single-flour alternatives for this recipe to keep the cupcakes tender and moist.
Can I make these cupcakes vegan?
This recipe can be adapted with a few swaps like flax eggs instead of regular eggs, and vegan yogurt and cream cheese alternatives. Keep in mind the texture may change slightly, but the lime and agave flavors will still shine.
How can I tell when the cupcakes are done?
Use a toothpick test by inserting it in the center; if it comes out clean or with just a few moist crumbs, they’re done. Also, the edges will look set and slightly pulled away from the pan.
Is the glaze necessary?
The lime glaze adds a nice finishing touch of extra tartness and sweetness, but the cupcakes are delicious even without it. If you prefer less sweetness, you can skip or lightly drizzle it instead.
Final Thoughts
There’s something so special about a cupcake that manages to be perfectly moist, bursting with citrus freshness, and naturally sweetened with agave—especially without gluten! I truly hope you enjoy making and sharing this Gluten-Free Lime Agave Cupcakes Recipe as much as I do. It’s the kind of treat that brings smiles, brightens your day, and makes every bite feel like sunshine. Happy baking!
Print
Gluten-Free Lime Agave Cupcakes Recipe
- Prep Time: 20 minutes
- Cook Time: 20 minutes
- Total Time: 40 minutes
- Yield: 12 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Gluten Free
Description
These Gluten Free Lime Agave Cupcakes are light, fluffy, and bursting with fresh lime flavor, sweetened naturally with agave syrup. Perfectly moist thanks to a blend of Greek yogurt and buttermilk, they’re topped with a tangy cream cheese swirl and finished with a zesty lime glaze. Ideal as a refreshing gluten-free dessert that doesn’t sacrifice taste or texture.
Ingredients
Cupcake Batter
- 1½ cups gluten-free flour blend (contains rice flour, tapioca starch, potato starch)
- ¼ cup arrowroot starch
- 1 teaspoon xanthan gum
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ¼ teaspoon salt
- 2 large eggs, room temperature
- ½ cup agave syrup
- ¼ cup coconut oil, melted and cooled
- ½ cup Greek yogurt
- ¼ cup buttermilk
- 1 tablespoon lime zest (from about 2 limes)
- 2 tablespoons fresh lime juice
Cream Cheese Swirl
- 4 ounces cream cheese, room temperature
- 2 tablespoons agave syrup
- 1 teaspoon lime zest
Lime Glaze
- 1 cup powdered sugar
- 2 tablespoons fresh lime juice
Instructions
- Preheat and Prepare: Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners. Using room-temperature eggs will help the batter emulsify better, which is crucial to the cupcakes’ rise.
- Mix Dry Ingredients: In a large bowl, whisk together the gluten-free flour blend, arrowroot starch, xanthan gum, baking powder, baking soda, and salt to distribute the leavening agents evenly and ensure a light cupcake texture.
- Combine Wet Ingredients: In a separate bowl, whisk the eggs and agave syrup until pale. Then stir in the melted coconut oil, Greek yogurt, buttermilk, lime zest, and lime juice, mixing just until combined to keep the batter tender.
- Combine Wet and Dry: Pour the wet ingredients into the dry mixture, gently folding until no streaks of flour remain. Avoid overmixing to prevent a dense cupcake.
- Prepare Cream Cheese Swirl: Beat together the cream cheese, agave syrup, and lime zest in a small bowl until smooth and lump-free for a tangy swirl inside the cupcakes.
- Assemble in Muffin Tin: Spoon about one tablespoon of batter into each muffin liner. Add a teaspoon of the cream cheese mixture on top, then cover with another tablespoon of batter. Use a skewer to gently swirl the cream cheese into the cupcake batter without overmixing.
- Bake: Bake in the preheated oven for 18 to 22 minutes, or until the edges are set and a toothpick inserted in the center comes out with a few moist crumbs. Do not overbake to avoid drying out the cupcakes.
- Cool: Let cupcakes cool in the pan for 5 minutes before transferring to a wire rack to cool completely, preserving their structure and preventing sogginess.
- Make Glaze: Whisk powdered sugar and fresh lime juice together until smooth and pourable. Adjust consistency by adding more sugar or lime juice as needed.
- Glaze Cupcakes: Once cupcakes are lukewarm, drizzle or dip the tops in the lime glaze. Let the glaze set before serving to achieve a beautiful, tangy finish.
Notes
- Use room temperature eggs and cream cheese to ensure smooth mixing and better texture.
- Do not overmix the batter to avoid dense, tough cupcakes.
- Adjust glaze consistency according to your liking—thicker glaze for dipping, thinner for drizzling.
- Make sure to swirl the cream cheese gently to avoid mixing it completely with the batter for a marbled effect.
- Store cupcakes in an airtight container in the refrigerator for up to 3 days; bring to room temperature before serving.

