by Olena

Healthy Vanilla Cupcakes

Olena's image
Olena Osipov
4.9 from 8 votes

Healthy Vanilla Cupcakes

These healthy vanilla cupcakes came out perfect! Because Easter is around the corner, we decorated them with unsulphured and unsweetened organic coconut flakes (fancy grade) for “feathers” and organic naturally coloured jelly beans for “eggs”. Kids were ecstatic as I never made cupcakes before!:)

I’m not a huge cake person and neither are my kids. They dislike the overly sweet icing but they sure love the cuteness of cupcakes. So, they were all over these cupcakes because they were up to their taste – low in sugar and healthy.

Healthy Vanilla Cupcakes close-up; Vanilla cupcake sliced in half with icing on top

Because these cupcakes are made with whole wheat flour, they are a tiny bit less fluffy but still very soft and moist! I would never think you can make healthy cupcakes with whole wheat flour and that is why I never attempted to. I assume using spelt flour will yield lighter cupcakes.

To keep cupcakes healthy I also used coconut oil, applesauce and maple syrup (honey works too). The icing is creamy and because it’s made with fresh ingredients, cupcakes should be refrigerated.

Looking for more healthy festive desserts? Try my healthy chocolate cake recipe, healthy strawberry cheesecake bars, or healthy chocolate mousse recipe.

Healthy Vanilla Cupcakes

Healthy Vanilla Cupcakes

Healthy Vanilla Cupcakes Recipe with whole wheat or spelt flour, coconut oil, applesauce, maple syrup, Greek yogurt frosting and are low in sugar.
4.88 from 8 votes
Print Save Rate
Prep Time: 10 minutes
Cook Time: 20 minutes
Servings: 12 cupcakes
Calories: 211kcal
Author: Olena Osipov


Wet Ingredients:

Dry Ingredients:


  • 1/2 cup cream cheese
  • 1/4 cup Greek yogurt plain (I used 2%)
  • 3 tbsp maple syrup or honey
  • 1/2 tsp pure vanilla extract



  • Preheat oven to 350 degrees F and spray non-stick 12 muffin tin with cooking spray or line with cupcake liners (these are awesome).
  • In a large mixing bowl, add Wet Ingredients and beat with a mixer until smooth. Add Dry Ingredients and process until smooth. Batter should be like for the cake consistency, thicker than for pancakes but thinner than for muffins. Pour batter into prepared muffin tin and bake for 20 minutes, or until tops spring back to the touch or a toothpick inserted in the middle comes out clean. Remove from the oven and let cool completely.
  • While cupcakes are baking, prepare icing by beating Icing ingredients in a medium bowl until smooth. Frost cupcakes, sprinkle with coconut flakes and place a few jelly beans in the middle (decorations are optional).

Store: Refrigerate in a glass airtight container for a few days.


    Serving: 1cupcake | Calories: 211kcal | Carbohydrates: 30g | Protein: 4g | Fat: 9g | Saturated Fat: 6g | Cholesterol: 38mg | Sodium: 246mg | Potassium: 105mg | Fiber: 2g | Sugar: 17g | Vitamin A: 167IU | Vitamin C: 1mg | Calcium: 89mg | Iron: 1mg
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    olena osipov in the studio

    Hello and welcome to iFOODreal.

    My name is Olena Osipov. I'm a mom to 2 boys, a wife to Alex and we reside on magical Vancouver Island in British Columbia, Canada. This is our healthy family recipes blog. Originally from Ukraine, I grew up on real food. As an adult, I struggled with diets for years because none worked long-term. Now for over 10 years, I cook easy healthy meals for my family. I can help you with “What’s for dinner?” too.

    24 comments on “Healthy Vanilla Cupcakes

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      1. You will need to add more sweetener and cacao powder. Not sure how much because I have not tested it. You can wing it if you wish. Icing might be more runny though because liquid sweetener but maybe cacao will offset it.

    1. 5 stars
      Hi Olena. Just writing again because I made these cupcakes last night and they taste absolutely delicious! I think I may make other versions with this batter like adding orange extract and others as I will definitely be keeping this as my go-to for cakes and cupcakes. So tasty!!!

    2. 4 stars
      Delicious! And they have my 6 year old’s seal of approval as the cupcakes for her birthday party. This is the third recipe I’ve tried and the best by far.
      How would I make the frosting slightly thicker? It’s a cupcake decorating birthday party and it’d be better thicker for sticking things on. Plus we live in a very hot climate!

    3. 5 stars
      So impressed with this recipe!! I’m always baking and referencing recipes posted online but have never left a comment before, this recipe is absolutely praise worthy. Prefect cake texture that’s moist, fluffy, and flavorful. I don’t eat dairy so I can’t comment on the frosting. I also substituted 2 tbsp of oil for the eggs and warm water for the milk. I couldn’t believe how quick and delicious these were. A huge hit with the whole family. Thank you!

    4. Is the honey/maple syrup for sweetening? We wanted to make a giant cupcake for our daughter and keep it on the healthy side, but she can’t eat honey/maple syrup.

    5. 5 stars
      Made these tonight & it was a much needed change from my weekly clean eating banana or pumpkin bread I usually make. While it’s not the same as a sinful vanilla cupcake it hits the spot for my dessert craving. Made peanut butter greek yogurt frosting & I’m in clean dessert heaven. Touch of sprinkles for my 4 year old who helped me make them & he doesn’t know these cupcakes are actually healthy. Just a mouthful of yum mommy these are goood. This one is a keeper.

      1. Hi Cindy. I know what you mean. These vanilla cupcakes are heavier and not as airy as original, understandable because of whole wheat flour. But definitely satisfy the craving. Your frosting sounds great!

      1. You need applesauce. I haven’t tested cupcakes with anything else and applesauce is quite irreplaceable when baking in regards acidity and dry:wet ratio.

    6. 5 stars
      I made these yesterday and they are so good! My question is I want to make them again but as mini cupcakes instead for my daughters birthday. Would the quantities be the same as the recipe?

      1. Hi Diana. Depends how many cupcakes you need or what is your pan size. I’m trying to remember the baking sheet and the only one I can think of is a 24 mini openings one. That is what I think this recipe will be sufficient for.

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