The Ultimate Healthy Red Velvet Cupcakes
Yields: 12 cupcakes
These truly are the BEST healthy red velvet cupcakes! They’re supremely tender, full of rich flavor, and topped with an irresistible sweet cream cheese frosting. The cupcakes are best if eaten the same day they’re made, but they’ll keep for at least three days if 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, cocoa powder, baking soda, and salt. In a separate bowl, whisk together the butter, egg whites, vanilla extract, butter extract, and vanilla stevia. Carefully stir in the red food coloring. Add in the Greek yogurt, stirring until no large lumps remain. Stir in the vinegar. Stir in the granulated stevia. 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 18-20 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, cream cheese, instant pudding, and vanilla 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: For the gluten-free flour, use the following blend: 1 cup (120g) millet flour, ½ cup (60g) tapioca flour, ½ cup (60g) brown rice flour, and 1 ½ teaspoons xanthan gum. Most store-bought gluten-free flour blends (like this one!) 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.

Do no use Dutched or special dark cocoa powder! They’re much less acidic than regular cocoa powder (like this), so the texture and flavor of these cupcakes won’t be the same.

Remember to measure the flour and cocoa powder correctly, using this method or a kitchen scale. (← That’s the one I own and love!) Too much of either will dry out your cupcake batter, and too much cocoa powder may make your cupcakes taste bitter.

The butter extract makes a big difference in how rich these cupcakes taste! This is the kind I use. Vanilla extract may be substituted for the butter extract, but the flavor of the cupcakes will be different.

I highly recommend using the vanilla stevia and granulated stevia! They’re some of my favorite ingredients (you’ll use them in all of these recipes of mine!). I buy my vanilla stevia online here because that’s the cheapest price I’ve found. I’ve bought the granulated stevia online here, and I’ve also found it in many Target and regular grocery stores on the baking aisle.

For sweeter cupcakes, increase the granulated stevia by an additional 2 tablespoons (12g). The baking time will increase by about 1-2 minutes.

If you prefer not to use stevia in the cupcakes, substitute 1 ½ cups (288g) of coconut sugar (or brown sugar or granulated sugar, if you’re not concerned about making the cupcakes “clean-eating friendly!”), and reduce the milk to 7-8 tablespoons (105-120mL). The baking time may vary with this substitution. If you prefer not to use the vanilla stevia in the frosting, then substitute ¼ cup of Truvia or granulated sugar.

Regular liquid red food coloring will give the brightest color. Liquid natural red food coloring may also be used, but the color will be more of a mahogany shade. I have not tried anything else (i.e. gel food coloring or beets) and don’t know how other options will turn out. If you don't want to use any food coloring at all, then replace the food coloring with water.

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 more classic spreadable (not pipe-able) cream cheese frosting that does NOT use instant pudding (and is clean-eating friendly), use this recipe of mine.

For red velvet cupcakes that have more vanilla flavor (and less of the “chocolaty vanilla” flavor that my taste testers and I preferred!), use 2 cups + 6 tablespoons (285) of white whole wheat flour and 2 tablespoons (10g) of cocoa powder instead.

For more information about the ingredients and why they’re required to create the best healthy red velvet cupcakes, please read my blog post above this recipe!

{gluten-free, clean eating option, low fat, low sugar}
Recipe by Amy's Healthy Baking at