These Gluten Free Lime Agave Cupcakes Recipe are a sparkling celebration of bright citrus flavor and natural sweetness, wrapped in a tender, moist crumb that’s free from gluten yet full of joy. Bursting with fresh lime zest and uplifted by a luscious agave syrup glaze, these cupcakes are proof that indulgence and wholesome ingredients can go hand in hand. Whether you’re baking for friends, family, or just because, this recipe turns simple pantry staples into a show-stopping treat that feels like sunshine on a plate.

Ingredients You’ll Need
The beauty of this Gluten Free Lime Agave Cupcakes Recipe lies in the straightforward but carefully selected ingredients that build layers of texture and flavor. Each element plays a key role, from the gluten-free flours creating a delicate crumb to the tangy lime zest that brightens every bite.
- 1½ cups gluten-free flour blend: A mix of rice flour, tapioca starch, and potato starch provides the perfect light, tender base.
- ¼ cup arrowroot starch: Adds extra crispness and helps with the cupcakes’ structure.
- 1 teaspoon xanthan gum: Essential for binding and to mimic gluten’s elasticity.
- 1 teaspoon baking powder: Your trusty leavening agent to give rise and fluff.
- ½ teaspoon baking soda: Works with acidic ingredients for perfect lift.
- ¼ teaspoon salt: Balances sweetness and enhances all the flavors.
- 2 large eggs, room temperature: Helps with structure and moisture; room temp ensures better mixing.
- ½ cup agave syrup: A natural sweetener that keeps these cupcakes moist and tender.
- ¼ cup coconut oil, melted and cooled: Brings a subtle tropical richness and a soft crumb.
- ½ cup Greek yogurt: Adds creaminess and a slight tang, making the cupcakes wonderfully moist.
- ¼ cup buttermilk: Works with baking soda to create a light texture and adds tangy depth.
- 1 tablespoon lime zest: Delivers a burst of fresh citrus aroma and flavor.
- 2 tablespoons fresh lime juice: Adds tang and balances the sweetness.
- 4 ounces cream cheese, room temperature: Used for the luscious swirled filling that surprises with creamy tanginess.
- 2 tablespoons agave syrup (for cream cheese swirl): Sweetens the cream cheese without overpowering its flavor.
- 1 teaspoon lime zest (for cream cheese swirl): Keeps the lime brightness consistent throughout.
- 1 cup powdered sugar (for glaze): Gives a sweet, smooth finish with a luxurious texture.
- 2 tablespoons fresh lime juice (for glaze): Makes the glaze tangy and pourable, harmonizing the cupcake flavors.
How to Make Gluten Free Lime Agave Cupcakes Recipe
Step 1: Prepare Your Oven and Muffin Tin
First things first, preheat your oven to 350°F and line your 12-cup muffin tin with paper liners. Using room-temperature eggs here is a smart move because they emulsify better with the other wet ingredients, which helps give your cupcakes an even rise and a lovely, tender texture.
Step 2: Combine Dry Ingredients
In a large bowl, whisk together your gluten-free flour blend, arrowroot starch, xanthan gum, baking powder, baking soda, and salt. This mix of ingredients ensures your leavening agents are evenly distributed and your cupcakes have a consistent texture without any dense patches.
Step 3: Mix Wet Ingredients
Next, in a separate bowl, beat the room temperature eggs and agave syrup until the mixture turns pale and slightly fluffy. Then, carefully stir in the melted coconut oil, Greek yogurt, buttermilk, lime zest, and lime juice. Mixing just until combined here is key—overmixing can make the batter tough, and we want these cupcakes silky and soft.
Step 4: Combine Wet and Dry Ingredients
Pour your wet ingredients into the dry bowl, then gently fold everything together until no flour streaks remain. The gentle folding helps maintain the lightness of the batter and prevents the cupcakes from becoming dense.
Step 5: Prepare the Cream Cheese Swirl
In a small bowl, beat the cream cheese with agave syrup and lime zest until perfectly smooth. This will create those delicious pockets of tangy sweetness that provide contrast and richness in every bite.
Step 6: Layer Batter and Cream Cheese
Spoon a level tablespoon of batter into each liner, add about a teaspoon of the cream cheese mixture on top, followed by another level tablespoon of batter. Use a skewer or toothpick to swirl the cream cheese gently into the top layer—just enough to make beautiful marbling without overmixing.
Step 7: Bake to Perfection
Pop your tray in the oven and bake for 18 to 22 minutes. You’ll know they are done when the edges set and a toothpick inserted in the center comes out with a few moist crumbs clinging to it. Be mindful not to overbake, or the cupcakes risk drying out.
Step 8: Cool the Cupcakes
Remove the cupcakes from the oven and let them cool in the pan for 5 minutes before transferring them to a wire rack. This step helps them set properly so the bottoms stay firm and not soggy.
Step 9: Make the Lime Glaze
While the cupcakes cool, whisk powdered sugar and fresh lime juice together until smooth. You want a glaze that’s pourable but not too thin, so adjust sugar or lime juice as needed for the perfect consistency.
Step 10: Glaze and Serve
Once the cupcakes are lukewarm, drizzle or dip them in the lime glaze for a glossy, tangy finish. Allow the glaze to set before serving for that extra-special touch.
How to Serve Gluten Free Lime Agave Cupcakes Recipe

Garnishes
For a charming presentation, sprinkle additional fresh lime zest or a few edible flowers on top of the glaze. You can also add a thin slice of lime or a small mint leaf for a pop of color and freshness that complements the cupcake’s zingy flavor.
Side Dishes
Pair these cupcakes with a light and refreshing cup of herbal tea, such as chamomile or green tea, to balance sweetness. A dollop of whipped coconut cream on the side can elevate the experience, especially if you’re serving these at an afternoon gathering or celebration.
Creative Ways to Present
Jazz up your cupcake display by serving them in a tiered stand decorated with fresh limes and greenery. Or place each cupcake in a bright, patterned liner that echoes the citrus theme. For fun, create mini cupcake “flights” with different flavored glazes alongside the lime for a tantalizing tasting experience.
Make Ahead and Storage
Storing Leftovers
Once cooled completely, store any leftover cupcakes in an airtight container at room temperature for up to 2 days. After that, refrigerate to keep them fresh for an additional 2 to 3 days. Keeping the glaze intact is easier if you let it fully set before storing.
Freezing
These cupcakes freeze brilliantly! Place them in a single layer on a baking sheet to freeze until firm, then transfer them to a freezer-safe container or bag. They can be frozen for up to 3 months. Thaw overnight in the fridge for best texture and flavor.
Reheating
If you want to enjoy your cupcakes warm, gently reheat them in the microwave for about 10 seconds or so—check to avoid overheating. This revives the softness without melting the glaze, giving you that fresh-from-the-oven feel.
FAQs
Can I substitute the agave syrup with honey?
Yes, honey can be used as a substitute, but it might slightly alter the flavor and sweetness. Agave syrup has a milder taste, so if you prefer honey, use a little less to keep the balance just right.
Is it necessary to use xanthan gum in this recipe?
Xanthan gum is important here as it mimics gluten’s binding properties, helping the cupcakes hold their shape and texture. If your gluten-free flour blend already contains xanthan gum, you can omit the extra teaspoon.
Can I make vegan versions of these cupcakes?
While this recipe relies on eggs and dairy for structure and creaminess, you could experiment with vegan substitutes like flax eggs and dairy-free yogurt. Just note that the texture and rise may differ slightly.
How can I prevent the cupcakes from drying out?
Be careful not to overbake and make sure to cool the cupcakes in the pan for a few minutes before moving them. Storage in an airtight container also helps retain moisture.
What’s the best gluten-free flour blend to use?
Look for a blend containing rice flour, tapioca starch, and potato starch for the most similar texture to this recipe’s original. Avoid blends heavy in almond or coconut flour, as they may change the cupcake’s crumb significantly.
Final Thoughts
If you’re looking for a bright, flavorful cupcake that’s both gluten free and naturally sweetened, this Gluten Free Lime Agave Cupcakes Recipe is an absolute winner. Its fresh lime zing paired with the creamy swirls and glossy glaze is pure magic. I hope you enjoy baking and sharing these delightful treats as much as I do—your kitchen is about to smell amazing!
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Gluten Free Lime Agave Cupcakes Recipe
- Prep Time: 15 minutes
- Cook Time: 22 minutes
- Total Time: 37 minutes
- Yield: 12 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Gluten Free
Description
These Gluten Free Lime Agave Cupcakes are a delightful treat combining a light, tender crumb with a tangy cream cheese swirl and a refreshing lime glaze. Perfectly sweetened with agave syrup and featuring the zest and juice of fresh limes, these cupcakes offer a moist, flavorful, naturally gluten-free dessert that’s ideal for any occasion.
Ingredients
Dry Ingredients
- 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
Wet Ingredients
- 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 and line a 12-cup muffin tin with paper liners. Using room-temperature eggs will help them emulsify easily, which is key for 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 until thoroughly combined. This ensures an even distribution of leavening agents and helps create a light, uniform texture.
- Combine Wet Ingredients: In a separate bowl, whisk the room-temperature eggs and agave syrup until the mixture appears pale. Stir in melted coconut oil, Greek yogurt, buttermilk, lime zest, and lime juice just until combined, avoiding overmixing to keep the batter tender.
- Combine Wet and Dry: Pour the wet mixture into the dry ingredients. Gently fold the batter until no streaks of flour remain. Take care not to overmix, as this can develop gluten, leading to a denser cupcake.
- Prepare Cream Cheese Swirl: In a small bowl, beat the room-temperature cream cheese, agave syrup, and lime zest until smooth and fully incorporated to avoid any lumps. This mixture will create delightful pockets of tangy flavor.
- Assemble Cupcakes: Spoon a level tablespoon of batter into each muffin liner. Add about 1 teaspoon of the cream cheese swirl on top of the batter, then layer with another level tablespoon of the cupcake batter. Use a skewer to gently swirl the cream cheese mixture into the top layer of batter, being careful not to overmix.
- Bake: Place the muffin tin in the preheated oven and bake for 18 to 22 minutes. They’re done when the edges are set, and a toothpick inserted in the center comes out with a few moist crumbs. Be careful not to overbake, which can dry them out.
- Cool: Remove the cupcakes from the oven and let them cool in the pan for 5 minutes before transferring them to a wire rack. Allowing them to cool slightly helps maintain their structure and prevents soggy bottoms.
- Prepare Glaze: While the cupcakes cool, whisk together powdered sugar and fresh lime juice in a small bowl until the mixture is smooth. The glaze should be pourable but not too runny; adjust the sugar or juice if necessary.
- Glaze Cupcakes: Once the cupcakes are lukewarm, drizzle or dip the tops in the lime glaze for a beautiful finish. Allow the glaze to set before serving.
Notes
- Ensure eggs and cream cheese are at room temperature for better mixing and texture.
- Do not overmix the batter to keep the cupcakes light and tender.
- Adjust the glaze consistency by adding more powdered sugar for thicker glaze or more lime juice for thinner glaze.
- Use gluten-free flour blends that already contain xanthan gum for best results, or add the xanthan gum as specified.
- Store cupcakes in an airtight container at room temperature for up to 2 days or refrigerate for up to 5 days.
- Bring refrigerated cupcakes to room temperature before serving for optimal texture and flavor.

