7 Healthy Cupcakes and Frosting Ideas You Need to Try

healthy cupcakes and frosting ideas

Are you looking for the perfect healthy cupcakes? Check out these cupcake and frosting variations to enjoy your favorite dessert guilt-free!

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Delicious Healthy Cupcakes

We’ve all heard about using black beans or chickpeas in healthy cake or cupcake recipes for a low-carb, higher protein option, but I bet most of you have never thought to use quinoa in a cupcake. With a basic vanilla cupcake recipe, you can make any of these substitutions below to customize your favorite dessert.

Healthy Cupcakes With Unsweetened Applesauce

As a common replacement for an egg in baking, a quarter-cup of unsweetened applesauce can be used to make an egg-free cupcake! However, some don’t know that it can replace butter or other fats for a low-fat dessert! This switch cuts calories and adds fiber to any recipe!

Since even unsweetened applesauce is naturally sweet, you can even decrease some of the sugar in your now healthier cupcakes! Use a 1:1 ratio to substitute applesauce for some or all of the butter in your recipes! (ex: if the recipe calls for a cup of butter, use 1/2 cup butter+ 1/2 cup applesauce, 1/4 cup butter, 3/4 cup applesauce, or just 1 cup applesauce)

Healthy Quinoa Cupcakes

I know, quinoa in cupcakes sounds bazaar, but it is a great way to add some whole grains to the cupcakes! Quinoa has about a third of the calories all-purpose flour does, plus quinoa is gluten-free and perfect if you are looking for a flowerless treat! Here’s a recipe for the yummiest flourless chocolate cupcakes made with quinoa!

healthy chocolate quinoa cupcakes

Healthier Gluten-Free Chocolate Quinoa Cupcakes

Delicious and nutritious healthy chocolate cupcakes the whole family will enjoy!
4.80 from 10 votes
Prep Time 10 minutes
Cook Time 19 minutes
Total Time 29 minutes
Course Dessert
Cuisine American
Servings 12 cupcakes
Calories 196 kcal


  • 2 eggs room temperature
  • 6 tbsp vegetable oil
  • 1 1/3 cup quinoa soaked in water overnight and drained
  • 1 tsp vanilla extract
  • 2/3 cup sugar
  • 3/4 cup unsweetened cocoa powder
  • 3/4 tsp baking powder
  • 1/4 tsp baking soda
  • 1/4 tsp salt


  • Preheat oven to 350 degrees. Grease or place cupcake liners in a cupcake tin.
  • Place wet ingredients and quinoa in a food processor or blender and blend until smooth.
  • In a separate bowl, mix the dry ingredients, then add egg, oil, and vanilla mixture.
  • Divide batter into cupcake tins and bake for about 19 minutes.
  • Allow them to cool on a cooling rack before icing with the frosting of your choice!


Calories: 196kcalCarbohydrates: 27gProtein: 5gFat: 9gSaturated Fat: 2gPolyunsaturated Fat: 5gMonounsaturated Fat: 2gTrans Fat: 1gCholesterol: 27mgSodium: 110mgPotassium: 199mgFiber: 3gSugar: 11gVitamin A: 42IUCalcium: 35mgIron: 2mg
Keyword dessert, gluten-free, healthy
Tried this recipe?Let us know how it was!

White Whole Wheat Flour Cupcakes

This is one of healthy baking’s best-kept secrets. If you substitute white whole wheat flour for all-purpose white flour in your favorite cupcake or cake recipe, you can increase the nutrient content without sacrificing a yummy taste. This substitution might take some experimenting if you are feeding picky eaters! At first, a 25 or 50% white whole wheat substitution in your cupcake won’t yield a noticeably different batter texture.

Maple Syrup Cupcakes

When thinking about your favorite dessert, the sugar content is often astronomical! The good news is, you can have your cake and eat it too when substituting maple syrup for sugar. You can use 3/4 cup of maple syrup instead of one cup of white sugar.

Since this is a liquid substitution, be sure to reduce the other liquids (oil, milk, etc.) in your recipe by around 3 TBSP. Depending on the flavor of your cupcakes, you may or may not want the maple flavor to be as pronounced. Keep in mind that the darker the syrup is, the stronger the maple flavor will be. Your waistline will thank you for making this substitution since it reduces both the calories and sugar content in your cupcakes!

Peanut Butter Cupcakes

Peanut butter can be a great replacement for butter to make any baked good a bit healthier! Using nut butter will increase the amount of protein in your cupcakes, give a nice nutty flavor, and significantly decrease cholesterol. I personally love using peanut butter in chocolate cupcakes! Who doesn’t love the classic peanut butter and chocolate combination?! These healthy cupcakes won’t be fat-free, but they are a lot lower in fat than a typical cupcake made with butter.

Healthy Frosting Swaps!

Greek Yogurt

We all love cream cheese frosting, but this healthier substitute is the ultimate icing on the cake! With only three ingredients, this frosting recipe is a must-try! All you need is 2 cups of full-fat Greek Yogurt, 2 teaspoons pure vanilla extract, and 1 cup of powdered sugar. Just strain the yogurt in the refrigerator overnight, then mix the ingredients with a handheld mixer. This pairs really nicely with a healthy carrot cake or red velvet cupcake! Most full-fat Greek yogurts have less than a third of the calories, a fifth of the fat, and a bit more protein than cream cheese.

Healthy Coconut Milk Frosting for Cupcakes

Using coconut milk in replacement of dairy is a safer option for my lactose-intolerant friends! One of my favorite coconut milk uses is in this dairy-free, vegan, 2- ingredient chocolate frosting!  Melt 3 cups of chocolate chips and stir in 1 cup of full-fat coconut milk. Then refrigerate the mixture until firm and beat until fluffy. For about half the calories of a heavy-whipping-cream-based frosting, this chocolatey frosting is a must in vegan baking! To keep this recipe gluten and dairy-free, make sure to use dairy-free, grain-free chocolate chips. For all my vegans out there, this frosting is great on a vegan chocolate cupcake!

The Best Healthy Cupcakes

These substitutions can work no matter what kind of cupcake you are trying to make a bit healthier! Be sure to share your favorite healthy swaps you made in your favorite cupcake recipe with your loved ones on FamilyApp!

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