by Olena

Healthy Vanilla Cupcakes

Olena's image
Olena Osipov
4.8 from 5 votes

This post contains affiliate links. Please see our disclosure policy.

How to make healthy vanilla cupcakes with whole wheat flour, no refined sugars, and a healthier yogurt and cream cheese based frosting!

Love nice and simple bakes? How about this almond flour cake, healthy chocolate cake, or healthy chocolate chip cookies?!

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! (especially when served alongside healthy lemon bars and carrot cake!) 🙂

These are low in sugar and healthier than regular cupcakes yet still sweet and flavorful! In fact, healthy cakes and muffins have become a new favorite of mine; and with healthy chocolate muffins, almond muffins, lemon zucchini muffins, and almond flour chocolate cake to choose from… well, who wouldn’t love to bake tons of healthier baked treats?!

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.

Check out my healthy zucchini muffin post to see a side-by-side comparison baking muffins with several types of flour!

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. Serve them up as a treat alone or enjoy alongside a healthy frappuccino or iced coffee!

More Healthy Dessert Recipes

Alternatively, you might want to browse through my entire collection of healthy muffin and quick bread recipes or my entire dessert collection!

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.
4.8 from 5 votes
Print Save Rate
Course: Dessert
Cuisine: American Ukrainian
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 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
    Join today and start saving your favorite recipes

    Recipes and images are a copyright of It is against the law to republish recipes anywhere including social media, print and all world wide web. Nutritional info is provided for informational purposes only and to the best knowledge.


    The information on this website is for educational purposes only. It has not been evaluated by the FDA and is not intended to diagnose, treat, prevent, or cure any disease. You assume full responsibility and liability for your own actions.

    This page may contain affiliate links. Please see our disclosure policy. is a participant of Amazon Services LLC Associates Program. If you make a purchase, we will receive a small commission at no extra cost to you. It helps keep iFOODreal recipes free. Thanks for your support!