Healthy Lemon Cupcakes with Lemon Frosting

Guilt-free lemon cupcakes topped with sweet swirls of lemon frosting! Easy to make & secretly healthy with no refined flour or sugar & just 128 calories!
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Healthy Lemon Cupcakes with Lemon Frosting

A few times during our childhood, Mom created an elaborate semi-homemade birthday cake for my brother, along with our help. We picked out a magazine with the cake layout my brother wanted at the grocery store, usually something like Women’s Day, and we purchased the rest of the necessary ingredients during that same trip.  

The recipes usually started with a boxed mix (Mom practically refused to bake anything from scratch except cookies!), split into three round pans to create a taller cake. While those cooled, we dyed some of the canned vanilla frosting blue with food coloring and prepared the fun embellishments.

Healthy Lemon Cupcakes with Lemon Frosting

Once Mom assembled the three layers, we spread plain vanilla frosting across half of the top of the cake, followed by the freshly dyed blue frosting on the remaining half and around the sides. We pressed small Goldfish crackers into the sides to make it appear like they were swimming in circles around the cake, and then we started decorating the top.

After crushing graham crackers into itty bitty crumbs, we sprinkled that on the plain white frosting as “sand.” We set a few gummy Lifesavers into the blue “ocean” patch on the top and gently pressed a Teddy Graham into the center each. We also cut small pieces of Fruit Stripe zebra gum as the Teddy Grahams’ “beach towels,” which rested on the plain frosting for when they finished splashing around in the water. Finally, we piped a little frosting onto the Teddy Grahams as “swim suits.”

Those cakes were so cute and fun to make! (I’m really sorry about that year Skipper got your cake though, bud!)

Healthy Lemon Cupcakes with Lemon Frosting

Although everyone would love making another one of those cakes for old time’s sake, my brother probably couldn’t enjoy it because of the many food allergies he has developed over the years… So I made these Healthy Lemon Cupcakes with Lemon Frosting for him instead! Lemon is his all-time favorite cake flavor, and he said these were absolutely full of that bright sunshiny flavor.

Even better? They contain no refined flour or sugar and only 128 calories! I don’t need a birthday as an excuse to celebrate that! ??

Healthy Lemon Cupcakes with Lemon Frosting

This healthy lemon cake base starts with white whole wheat flour (like this). White whole wheat flour is made exactly the same way as regular whole wheat flour! It just comes from a special type of soft white wheat, whereas regular whole wheat flour is made from heartier red wheat. This gives white whole wheat flour the same health benefits as regular whole wheat flour, but with its lighter taste and texture, it’s perfect for these cupcakes!

With just 1 tablespoon of butter or coconut oil, you’ll mix Greek yogurt into the batter for the rest of that classic tender cupcake texture. If you’ve been around my blog for a while, you know how much I love Greek yogurt! It adds the same moisture as butter or oil for a fraction of the calories, and it gives your baked treats a protein boost, too!

Of course, we can’t forget the true star of these cupcakes… The lemons! You’ll use both lemon zest and freshly squeezed lemon juice in the cupcake batter. The former actually provides the majority of the citrus flavor, so don’t skimp on it! If you can find Meyer lemons, I highly recommend them. They’re brighter and sweeter than traditional lemons!

Healthy Lemon Cupcakes with Lemon Frosting
Healthy Lemon Cupcakes with Lemon Frosting

Now this frosting has a secret… It’s actually made from more Greek yogurt! And because of that, you’ll use lemon extract (like this) to flavor the frosting. No lemon juice here—that would just make the yogurt curdle! To make the frosting stiff enough to pipe into those elegant swirls, you’ll beat the Greek yogurt with instant vanilla pudding mix (like this). Such a fun and nifty trick!

To sweeten both the cupcakes and the frosting, you’ll use one of my favorite ingredients: vanilla crème stevia. Stevia is a plant-based, no-calorie sweetener that contains nothing refined or artificial (aka it’s clean-eating friendly!). A little goes a long way! This is the kind I use because I love its warm vanilla flavor. Although you can find it at many health-oriented grocery stores, I always buy mine online here because that’s the cheapest price I’ve found. (And you’ll use it in all of these recipes of mine, too!)

Healthy Lemon Cupcakes with Lemon Frosting

Happy birthday, bud! ??? And when you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! ?) I’d love to see your cupcakes and feature them in my Sunday Spotlight series!

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Healthy Lemon Cupcakes with Lemon Frosting
3.0 from 4 reviews

Yields: 12 cupcakes
These cupcakes are perfect for anyone who loves lemon! My brother absolutely loves them, and lemon is his all-time favorite cake flavor. The cupcakes can be made up to 3 days in advance and stored in an airtight container on the counter, and the frosting can be made up to 1 week in advance and stored in an airtight container in the refrigerator. The cupcakes are best if eaten the same day they’re frosted (and ideally, the same day they’re made, too!), but leftover frosted cupcakes may be stored in an airtight container in the refrigerator.
  • for the cupcakes
  • 2 ½ cups (300g) white whole wheat flour or gluten-free* flour (measured like this)
  • 1 ½ tsp baking powder
  • ½ tsp baking soda
  • ½ tsp salt
  • 3 tbsp (15g) lemon zest*
  • 1 tbsp (14g) coconut oil or unsalted butter, melted
  • 3 large egg whites, room temperature
  • 1 tbsp (15mL) vanilla extract
  • 1 tbsp (15mL) vanilla crème stevia
  • ½ cup (120g) plain nonfat Greek yogurt
  • ½ cup + 2 tbsp (150mL) freshly squeezed lemon juice
  • ½ cup (120mL) nonfat milk
  • for the frosting
  • 2 cups (480g) plain nonfat Greek yogurt
  • 2 servings (16g) sugar-free, fat-free instant vanilla pudding mix (see Notes)
  • 2 tsp lemon extract
  • ⅞ tsp vanilla crème stevia, or more/adjusted to taste
  1. To prepare the cupcakes, preheat the oven to 350°F. Line 12 muffin cups with paper liners, and coat the liners with cooking spray.
  2. In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. Whisk in the lemon zest. In a separate bowl, whisk together the coconut oil, egg whites, vanilla, and vanilla crème stevia. Stir in the Greek yogurt. Stir in the lemon juice. Alternate between adding the flour mixture and the milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
  3. Divide the batter between the prepared paper liners. Bake at 350°F for 19-22 minutes or until the centers feel firm to the touch and a toothpick inserted into the center comes out clean. Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
  4. While the cupcakes bake, prepare the frosting. Add the Greek yogurt, instant pudding, lemon extract, and vanilla crème stevia to a large bowl. Beat with an electric mixer for 2 minutes. Cover the top of the bowl with foil, and refrigerate for at least 2 hours. Once the cupcakes have completely cooled, pipe the cream cheese frosting on top just before serving.
Notes: Do not use a stand mixer or electric hand-held mixer for this recipe. Use a whisk where instructed and a fork or spoon for everything else.

For the gluten-free flour, use the following blend: 1 ¼ cups (150g) millet flour, ¾ cup (90g) tapioca flour, ½ cup (60g) brown rice flour, and 1 ¾ teaspoons xanthan gum. Most store-bought gluten-free flour blends should work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour or all-purpose flour may be substituted for the white whole wheat flour.

I highly recommend using Meyer lemons, if you can find them! They’re brighter and sweeter in flavor compared to traditional lemons.

I highly recommend using the vanilla crème stevia! It’s one of my favorite ingredients (you’ll use it in all of these recipes of mine!), and I buy it online here because that’s the cheapest price I’ve found. If you prefer not to use stevia in the cupcakes, substitute ¾ cup (180mL) of agave, honey, or pure maple syrup for the vanilla crème stevia. Omit the milk and 2 tablespoons of lemon juice. (The batter should be fairly thick, similar to muffin batter.) If you prefer not to use the vanilla crème stevia in the frosting, then substitute 1 ¾ teaspoons of this powdered stevia OR 6-8 tablespoons of Truvia or granulated sugar.

Any milk may be substituted for the nonfat milk.

You just need the dry instant pudding mix—don’t prepare it according to the package directions! For a spreadable (not pipe-able) frosting, you may omit the instant pudding mix.

You’re using lemon extract in the frosting because lemon juice or lemon zest would cause the Greek yogurt to curdle. (Not good!) For a mellower frosting flavor, decrease the lemon extract to 1 ¾ teaspoons.

{gluten-free, clean eating option, low fat, low sugar}


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   Simple Strawberry Lemon Cake
   Simple Raspberry Lemon Cake
   Healthy Banana Cupcakes with Cream Cheese Frosting
   Healthy Blueberry Cupcakes with Cream Cheese Frosting

Healthy Lemon Cupcakes with Lemon Frosting

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