Keto Lemon Cupcakes – Bright, Zesty, and Low-Carb

Love a citrusy dessert but want to keep it low-carb? These keto lemon cupcakes hit that sweet, tangy spot without the sugar crash. They’re soft, fluffy, and full of real lemon flavor, with a creamy lemon frosting that ties it all together.

The batter comes together quickly, and the ingredients are easy to find. Whether you’re new to keto baking or a seasoned pro, this recipe is simple, reliable, and satisfying.

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Keto Lemon Cupcakes - Bright, Zesty, and Low-Carb

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Prep Time 15 minutes mins

Cook Time 20 minutes mins

Total Time 35 minutes mins

Servings: 12 servings

Ingredients Method

Ingredients

  

• 1 1/2 cups fine blanched almond flour
• 2 tablespoons coconut flour
• 1/2 cup granulated erythritol or allulose (plus more to taste)
• 2 teaspoons baking powder
• 1/4 teaspoon fine sea salt
• 3 large eggs, room temperature
• 1/3 cup unsalted butter, melted and slightly cooled (or coconut oil)
• 1/3 cup full-fat Greek yogurt or sour cream
• 2 tablespoons fresh lemon zest (from about 2 lemons)
• 3 tablespoons fresh lemon juice
• 1 teaspoon pure vanilla extract
• 4 ounces cream cheese, softened
• 1/4 cup unsalted butter, softened
• 1/3–1/2 cup powdered erythritol or powdered allulose, to taste
• 1–2 tablespoons fresh lemon juice
• 1 teaspoon lemon zest
• 1/2 teaspoon vanilla extract
• Pinch of salt

Method

 

1. Prep your pan and oven. Line a 12-cup muffin pan with paper liners. Preheat the oven to 350°F (175°C).
2. Mix the dry ingredients. In a large bowl, whisk almond flour, coconut flour, granulated sweetener, baking powder, and salt until evenly combined.
3. Whisk the wet ingredients. In a separate bowl, whisk eggs, melted butter, yogurt, lemon zest, lemon juice, and vanilla until smooth.
4. Combine gently. Pour the wet mixture into the dry. Stir with a spatula until just combined. The batter will be thick but scoopable. If it seems too thick, add 1–2 tablespoons of almond milk or water.
5. Fill the liners. Divide the batter evenly among the 12 liners, about 3/4 full. Smooth the tops with the back of a spoon.
6. Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
7. Cool completely. Let cupcakes cool in the pan for 5 minutes, then transfer to a rack to cool fully before frosting.
8. Make the frosting. Beat cream cheese and butter until creamy. Add powdered sweetener, lemon juice, zest, vanilla, and a pinch of salt. Beat until fluffy. Adjust sweetness and lemon to taste.
9. Frost and finish. Spread or pipe frosting onto cooled cupcakes. Garnish with extra zest or a thin lemon slice if you like.

Why This Recipe Works

• Almond flour gives structure while keeping the cupcakes tender and moist. It’s naturally low-carb and works well with citrus flavors.
• Coconut flour adds lift and helps the batter hold its shape, preventing dense or soggy cupcakes.
• Lemon zest and juice deliver bright flavor without extra carbs or artificial taste.
• Greek yogurt or sour cream adds moisture and a little tang, so the cupcakes don’t dry out.
• Erythritol or allulose sweetens without spiking blood sugar, and both bake well in cupcakes.

Ingredients

• 1 1/2 cups fine blanched almond flour
• 2 tablespoons coconut flour
• 1/2 cup granulated erythritol or allulose (plus more to taste)
• 2 teaspoons baking powder
• 1/4 teaspoon fine sea salt
• 3 large eggs, room temperature
• 1/3 cup unsalted butter, melted and slightly cooled (or coconut oil)
• 1/3 cup full-fat Greek yogurt or sour cream
• 2 tablespoons fresh lemon zest (from about 2 lemons)
• 3 tablespoons fresh lemon juice
• 1 teaspoon pure vanilla extract

For the Lemon Frosting:

• 4 ounces cream cheese, softened
• 1/4 cup unsalted butter, softened
• 1/3–1/2 cup powdered erythritol or powdered allulose, to taste
• 1–2 tablespoons fresh lemon juice
• 1 teaspoon lemon zest
• 1/2 teaspoon vanilla extract
• Pinch of salt

Step-by-Step Instructions

1. Prep your pan and oven. Line a 12-cup muffin pan with paper liners.

   Preheat the oven to 350°F (175°C).

2. Mix the dry ingredients. In a large bowl, whisk almond flour, coconut flour, granulated sweetener, baking powder, and salt until evenly combined.
3. Whisk the wet ingredients. In a separate bowl, whisk eggs, melted butter, yogurt, lemon zest, lemon juice, and vanilla until smooth.
4. Combine gently. Pour the wet mixture into the dry. Stir with a spatula until just combined. The batter will be thick but scoopable.

   If it seems too thick, add 1–2 tablespoons of almond milk or water.

5. Fill the liners. Divide the batter evenly among the 12 liners, about 3/4 full. Smooth the tops with the back of a spoon.
6. Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
7. Cool completely. Let cupcakes cool in the pan for 5 minutes, then transfer to a rack to cool fully before frosting.
8. Make the frosting. Beat cream cheese and butter until creamy. Add powdered sweetener, lemon juice, zest, vanilla, and a pinch of salt.

   Beat until fluffy. Adjust sweetness and lemon to taste.

9. Frost and finish. Spread or pipe frosting onto cooled cupcakes. Garnish with extra zest or a thin lemon slice if you like.

How to Store

• Refrigerator: Store frosted cupcakes in an airtight container for up to 5 days.

  They taste best when brought to room temperature for 10–15 minutes before serving.

• Freezer: Freeze unfrosted cupcakes for up to 2 months. Wrap individually, then place in a freezer bag. Thaw at room temperature and frost fresh.
• Frosting: Keep extra frosting in the fridge for up to 1 week.

  Re-whip briefly if it firms up.

Why This is Good for You

• Low in carbs: Almond and coconut flours keep net carbs low, making these cupcakes keto-friendly.
• Healthy fats: Butter, cream cheese, and almond flour provide satiating fats that help curb cravings.
• No refined sugar: Using erythritol or allulose avoids blood sugar spikes and crashes.
• Lemon perks: Fresh lemon adds flavor and brightness without extra calories or carbs.

Pitfalls to Watch Out For

• Overbaking: Keto cupcakes can dry out fast. Start checking at 18 minutes and pull them as soon as they’re set.
• Skipping room temperature ingredients: Cold eggs or yogurt can seize the butter and lead to a lumpy batter.
• Using coarse almond meal: You need fine blanched almond flour for a light, tender crumb.
• Too much lemon juice: Acid affects structure. Stick to the amounts listed or add a touch more coconut flour if increasing juice.
• The wrong sweetener: Granulated erythritol can crystallize if used in frosting.

  For the frosting, powdered sweetener works best.

Variations You Can Try

• Lemon-Blueberry: Fold in 1/2 cup fresh blueberries (pat dry). Toss them in a teaspoon of almond flour to prevent sinking.
• Lemon Poppy Seed: Add 1 tablespoon poppy seeds to the batter for a bakery-style twist.
• Lemon Coconut: Stir 1/3 cup unsweetened shredded coconut into the batter and top with toasted coconut flakes.
• Lemon Strawberry: Top frosted cupcakes with sliced fresh strawberries and a tiny pinch of lemon zest.
• Dairy-Free: Use coconut oil instead of butter and coconut cream instead of yogurt. For frosting, use a dairy-free cream cheese alternative.
• Extra Tangy: Add 1/4 teaspoon citric acid to the frosting for a sharper lemon punch.

FAQ

Can I use only almond flour and skip coconut flour?

Yes, but the texture will be slightly heavier.

If you skip the coconut flour, increase almond flour by about 1/4 cup and watch the bake time. The cupcakes may be a bit more moist and dense.

What’s the best keto sweetener for these cupcakes?

Erythritol and allulose both work. Allulose tends to keep cakes softer and moister, while erythritol offers a cleaner sweetness but can be slightly cooling.

For frosting, use powdered sweetener to avoid graininess.

Do I need paper liners?

Liners help with release and keep the cupcakes from sticking. If you’re skipping liners, grease the pan very well and let cupcakes cool completely before removing.

Can I make these ahead?

Absolutely. Bake the cupcakes a day ahead and store them covered at room temperature if unfrosted.

Refrigerate after frosting. You can also freeze the unfrosted cakes and frost the day you serve.

How do I make them more lemony?

Add extra zest to both batter and frosting. You can also use a few drops of lemon extract, but go light—extracts can taste artificial if overused.

Why did my cupcakes sink?

This usually comes from underbaking, too much liquid, or opening the oven door early.

Measure lemon juice carefully and bake until fully set in the center.

Can I make them into a mini version?

Yes. Use a mini muffin pan and bake for 10–12 minutes, checking early. Frost lightly or simply dust with powdered sweetener if you prefer.

Wrapping Up

These keto lemon cupcakes bring a bright, bakery-style treat to your low-carb routine.

They’re easy to make, use simple ingredients, and deliver real lemon flavor in every bite. Keep a batch in the fridge for quick desserts, or dress them up for a special occasion. With a few small tweaks and smart storage, they’ll quickly become a favorite go-to recipe.

Enjoy the zest and the simplicity—no sugar required.