How to Make Gluten Free Lime Agave Cupcakes

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Gluten free lime agave cupcakes feature a gluten-free flour blend, agave syrup, lime zest and a cream cheese swirl, from a warm 350°F oven. A simple lime glaze gives them a shine; serve warm with fresh berries.

This recipe addresses dryness in gluten-free baking, enhances flavor with lime, and reduces prep time for quick, enjoyable treats.

Four pink-frosted cupcakes with white sprinkles on a marble surface.

I’ve battled dry gluten free cupcakes before, especially on busy weeknights with my kids begging for snacks. I once undermeasured arrowroot (oops!) but this easy lime cupcakes blend fixed that. The zesty scent actually brightened an otherwise hectic evening.

This recipe uses agave and a mix of yogurt and buttermilk for lasting moisture, while arrowroot keeps edges firm. Cupcakes bake in 18 to 22 minutes and cool in 5 minutes, giving a soft center and a just-right crust that holds its shape.

If you want another easy gluten-free bake, try my Gluten Free Chocolate Chip Cookies.

Dietary Considerations

  • This recipe is gluten-free thanks to a certified gluten-free flour blend.
  • This recipe is not dairy-free due to Greek yogurt and cream cheese.
  • This recipe is not vegan due to eggs and cream cheese.
  • This recipe is not keto or low-carb due to agave syrup and gluten-free flour.
  • This recipe is nut-free as it contains no nuts or nut byproducts.

Why You Will Love This Recipe

  • Light, moist crumb Thanks to gluten-free flour, arrowroot starch, Greek yogurt and buttermilk, these gluten free lime agave cupcakes hold a tender crumb that remains soft for days.
  • Really bright lime zing Fresh lime zest, juice and a simple glaze layer deliver clear citrus notes without extra sugar load, fitting my diabetic-friendly sweet cravings.
  • Cream cheese swirl surprise A lime-scented cream cheese ribbon threads through each cake, adding tangy moisture and a smooth bite that balances the agave sweetness.
  • Quick mix-and-go This Easy Lime Cupcakes recipe takes under ten minutes of mixing before baking, so I can have fresh cupcakes ready in about twenty minutes.

Print

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Three gluten-free cupcakes with pink frosting and white pearls on cake stands.

Gluten Free Lime Agave Cupcakes

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  • Author: Charlene
  • Prep Time: 15 minutes
  • Cool Time: 5 minutes
  • Cook Time: 20 minutes
  • Total Time: 40 minutes
  • Yield: 12 cupcakes 1x
  • Category: dessert
  • Method: baking
  • Cuisine: American
  • Diet: gluten-free

Description

Delicious gluten-free lime agave cupcakes with a cream cheese swirl and lime glaze, perfect for a sweet treat.


Ingredients

Scale
  • 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
  • 4 ounces cream cheese, room temperature
  • 2 tablespoons agave syrup (for cream cheese swirl)
  • 1 teaspoon lime zest (for cream cheese swirl)
  • 1 cup powdered sugar (for glaze)
  • 2 tablespoons fresh lime juice (for glaze)

Instructions

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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

  • Make sure to incorporate xanthan gum and arrowroot starch as they play critical roles in preventing crumbling and maintaining structural integrity in gluten-free baking.
  • Greek yogurt and buttermilk contribute to the moisture needed to keep these cupcakes tender over time, so don’t skip either ingredient.
  • The cream cheese swirl not only adds richness but also visual appeal, providing a delightful contrast to the light lime cake.
  • For storage, keep the cooled cupcakes at room temperature in an airtight container for up to 2 days. You can also freeze them without glaze for up to 1 month. Thaw in the refrigerator when you’re ready to enjoy, then glaze before serving.
  • If you want to make these cupcakes dairy-free, try swapping the cream cheese with a non-dairy alternative and using plant-based yogurt instead. However, keep in mind that this may alter the texture slightly.

Nutrition

  • Serving Size: 1 cupcake
  • Calories: 180
  • Sugar: 12g
  • Sodium: 150mg
  • Fat: 7g
  • Saturated Fat: 4g
  • Unsaturated Fat: 2g
  • Trans Fat: 0g
  • Carbohydrates: 25g
  • Fiber: 1g
  • Protein: 3g
  • Cholesterol: 40mg

Three gluten-free cupcakes with pink frosting on two-tiered stands.

Ingredient Notes

  • Gluten-free flour blend: choose rice flour, tapioca starch, potato starch blend for gluten free lime agave cupcakes; smooth texture; binds well; avoid gritty crumbs.
  • Arrowroot starch: crisp edges, light structure; fine powder; store in cool, dry place; no direct substitute.
  • Xanthan gum: use 1 teaspoon; improves binding; store airtight; key for crumb stability; no substitute.
  • Baking powder: acts with acid; use fresh for lift; check expiration; evenly distribute through the mix.
  • Baking soda: reacts with buttermilk; boosts rise; whisk into dry mix; make sure it’s not clumped.
  • Salt: balances flavors; fine-grain table salt works; stir thoroughly; prevents bland taste.
  • Eggs: room temperature large eggs; whisk easily with agave; keep shells free of cracks; binds ingredients.
  • Agave syrup: liquid sweetener; provides moisture; choose light agave; substitute honey if needed.
  • Coconut oil: melted and cooled; neutral flavor; set aside to avoid hot spots; swap melted butter if preferred.
  • Greek yogurt: full-fat; thick texture adds moisture; bring to room temp; use plain to avoid off-flavors.
  • Buttermilk: acidic boost for lift; stir before measuring; shake container; pour from bottom so solids mix evenly.
  • Lime zest: finely grated; avoid white pith; zest green peel only; refrigerate briefly; releases citrus oils.
  • Lime juice: fresh-squeezed; strain seeds; adjust amount to taste; bottled lacks bright zing.
  • Cream cheese: room temperature block; softens quickly; beat with agave and zest; choose full-fat for tang.
  • Powdered sugar: sift before mixing; fine texture prevents glaze lumps; store airtight to avoid clumps.

Recipe Baking Tips

  1. When edges brown too fast 15 minutes into baking, tent pan with foil and continue until 22 minutes.
  2. If glaze runs off tops, whisk in 1 tablespoon extra powdered sugar and rest 5 minutes before glazing.
  3. If cream cheese swirl sinks to bottom, chill mixture 10 minutes before swirling into batter.
  4. If crumb feels gummy after baking, fold batter with 10 gentle strokes before adding swirl.
  5. If cupcakes dry after one day, place a damp paper towel inside a 2-quart airtight container.

Serving Suggestions

Serve with gluten free garlic bread and zucchini bread alongside a mixed greens salad dressed with lemon vinaigrette and toasted pumpkin seeds. Pair cupcakes with cilantro lime rice served alongside black bean salad mixed with red onion, cilantro, and lime juice for added acidity and color.

Use cupcakes to build summer berry trifle with coconut whipped cream and macerated strawberries layered in a clear glass dish. Add pieces of cupcakes to yogurt parfait alongside chopped kiwi, mango, and granola, then drizzle extra lime glaze over the top before serving.

Top cupcakes with lime glaze, sprinkle toasted coconut flakes or chopped pistachios, and finish with extra fresh lime zest before serving to enhance citrus notes. Drizzle coconut caramel sauce or honey agave sauce around dessert plates, add mint sprigs or edible flowers for a decorative finish that complements the lime flavor.

Recipe variations

  • You can use 1½ cups almond flour instead of the gluten-free flour blend for a nuttier crumb.
  • Add 1 teaspoon poppy seeds or 2 tablespoons shredded coconut for flavor like my Gluten Free Lemon Zucchini Bread.
  • Either coconut oil or ¼ cup melted unsalted butter can replace the oil in this wet mix.
  • If using a second muffin tin, double the batter to bake 24 cupcakes with 2 tins.

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How to Store?

To keep your gluten free lime agave cupcakes fresh and delicious, follow these storage tips:

Room Temperature: Store in an airtight container at room temperature up to 2 days.

Refrigeration: Place in an airtight container in the refrigerator up to 5 days.

Freezing: Wrap each cupcake in plastic wrap or aluminum foil. Place in a freezer bag up to 1 month. Thaw in the refrigerator before adding glaze.

If you enjoyed this Gluten Free Lime Agave Cupcakes or any other recipe on my blog, please leave a ⭐ star rating and let me know how it went in the comments below. Thanks for visiting!

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