Healthy Lemon Cupcakes with Lemon Frosting
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.
  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}
Recipe by Amy's Healthy Baking at