These Healthy Vanilla Cupcakes are moist, light and fluffy. They are also lower in sugar thanks to maple syrup and are topped with healthier buttercream frosting!

Also you might love this moist cake with almond flour!

Healthy cupcakes topped with buttercream frosting and sprinkles.

These healthy vanilla cupcakes are our mostly go-to for kids events. Kids love cupcakes and I find they want them to be light, airy and moist like conventional ones.

Kids are smart and not easy to trick. These mini cakes will deliver!

The main characteristic of my healthy vanilla cupcakes recipe is that they are made with almond flour instead of all-purpose flour. It is light in flavor and has a similar soft texture. It also keeps them moist along with the yogurt.

For healthier cupcakes, we do not omit sugar completely but rather use only 1/2 cup of maple syrup instead. So the only way they will have your kids bouncing off the walls is from pure joy!

Frosted vanilla cupcakes with one unwrapped from liner and cut in half.

Ingredients for Healthy Vanilla Cupcakes

Here is a quick glance at ingredients you will need to make this recipe.

  • Eggs: Needed for binding the ingredients together so these healthy vanilla cupcakes don’t crumble.
  • Maple syrup: Full of antioxidants, vitamins, and minerals. You can use honey instead if preferred.
  • Greek yogurt: Yogurt replaces what butter and oil do in traditional cupcake recipes.
  • Vanilla extract: A vanilla flavor that enhances each surrounding ingredient maximizing taste.
  • Lemon zest: A bright burst of citrus zest strikes a nice balance to all the warm flavors. You can also use lime or orange.
  • Baking powder & baking soda: The leavening agents that work together to give cupcakes their rise.
  • Salt: As you probably know, salt is another incredible flavor enhancer.
  • Almond flour: I use superfine almond flour. You can buy it in any store or here is how to make almond flour at home.
  • Cooking spray
Almond flour, yogurt, eggs, lemon, maple syrup, baking soda, baking powder, vanilla, salt.

How to Make Healthy Vanilla Cupcakes

One of the best things about this healthy vanilla cupcake recipe is there is no need for an electric mixer.

It can all be done by hand with a whisk making it easy even for small kids to help. Full recipe card is located at the bottom.

Liquid ingredients whisked in a bowl.
  • Combine everything except the almond flour: In a large bowl, whisk together eggs, maple syrup, yogurt, vanilla extract, lemon zest, baking powder, baking soda, and salt. Make sure there are no lumps.
Cupcake batter in a glass bowl with metal whisk.
  • Add the flour: To the mixture, add the almond flour and use a spatula to stir gently. Mix well until everything has combined. The batter will be runnier than your average muffin batter but not quite as thick as the pancake batter. Basically like a cake batter!
Baked healthy cupcakes in a blue muffin tin.
  • Divide the batter and bake: Using an ice cream scoop, add equal amounts of batter into each of the 12 prepared muffin grooves and level with spatula. Bake on the middle rack for 20 minutes.

Use a toothpick to insert it into the center of the cupcake. If it comes out clean, it’s ready. It’s important to let cupcakes cool completely on a wire rack if you plan on adding any frosting.

Easy Healthy Frosting Options

When it comes to frosting your healthy vanilla cupcakes, just make sure they are completely cooled and use the frosting that will hold up. Here are a few suggestions:

Tips for the Best Results

  • A liquid sweetener is a must for new bakers: The reason for this is it’s important to keep the liquid to dry ingredient ratio. If you’re a more experienced baker and think you’d be able to use a dry sweetener like sugar, go for it. I think it will work.
  • Lower sugar cupcakes: It is possible to reduce maple syrup to 1/3 cup.
  • Sour cream: You can use sour cream instead of Greek yogurt.
  • Filling the batter: You want to make sure all of the cupcakes are equal in size so that they bake evenly.
  • Bake on a middle rack: Almond flour burns fast. I find most success with baking all almond flour recipes on the middle rack and lower oven temperature like 325 F degrees.
  • Do not overbake: Check on healthy vanilla cupcakes even 3-5 minutes before 20 minutes is up. But do not open the oven, just turn on the light.
Healthy cupcakes decorated with healthy frosting and sprinkles.

How Long Do They Keep?

Store leftovers: If you plan to store or freeze your healthy vanilla cupcakes for later on, do not frost them. If left unfrosted, you can keep the cupcakes stored at room temperature, loosely covered in a container, for up to 3 days.

If you want to keep them a little longer, transfer them to the fridge for up to 1 week. Store cupcakes that have frosting on them in the fridge for up to 3 days.

Can I Make Cupcakes Ahead of Time?

You can prepare the batter ahead of time. Just combine all of the ingredients, except baking powder and baking soda, cover and refrigerate until the next day.

When ready to bake, add in the leavening agents and follow the recipe.

Can I Freeze Them?

Yes, healthy vanilla cupcakes freeze well for up to 3 months! Be sure to freeze only unfrosted cupcakes. Layer them with parchment paper in a freezer-friendly bag. Take out what you need at a time and enjoy!


Can I use any other flour?

Unfortunately you cannot use any other flour like gluten free flour, all-purpose flour or whole wheat flour. Almond flour is quite unique.

Can I make healthy vanilla cupcakes as a cake?

Try my healthy birthday cake with very similar ingredients.

How do I prevent cupcakes from sticking to the liners?

I highly recommend to use parchment paper muffin liners because almond flour is delicate and muffins tend to stick even to the most well sprayed and even silicone cavities of a muffin tin.

Is there an egg substitute?

While I haven’t tried, feel free to give flax egg a go. Let me know in comments below if you try.

More Healthy Dessert Recipes

Looking down at healthy vanilla cupcakes with frosting and sprinkles.
Healthy vanilla cupcakes with icing and sprinkes

Healthy Vanilla Cupcakes

These Healthy Vanilla Cupcakes are moist, light and fluffy. They are also lower in sugar thanks to maple syrup and are topped with healthier buttercream frosting!
4.91 from 10 votes
Servings 12 cupcakes
Calories 223
Prep Time 10 minutes
Cook Time 20 minutes
Cooling Time 1 hour
Total Time 1 hour 30 minutes



  • Preheat oven to 325 degrees F. Line 12 muffin tin with parchment paper muffin liners and spray with cooking spray. Set aside.
  • In a large bowl, add eggs, maple syrup, yogurt, vanilla extract, lemon zest, baking powder, baking soda and salt. Whisk very well until combined and no lumps.
  • Add almond flour (make sure to level the top with knife and do not pack) and stir gently with spatula until well mixed. Batter will be runny.
  • Using an ice cream scoop, divide batter between 12 openings of previously prepared muffin tin and flatten with spatula. Bake on the middle rack for 20 minutes or until the toothpick inserted in the center comes out clean.
  • Remove from the oven, let cool for 15 minutes, then transfer to a wire rack to cool off completely before frosting.



  • Make Ahead: You can prepare the batter, minus the leavening agents, up to a day in advance. Refrigerate and mix in the baking powder and soda before baking.
  • Storing: Store unfrosted cupcakes at room temperature for 2-3 days or within the refrigerator for 5-7 days. Refrigerate frosted cupcakes for 3 days.
  • Freezing: Freeze unfrosted cupcakes in layers with parchment paper between, in a large freezer bag for up to 3 months.
  • Use liners: I highly recommend to line because almond flour is delicate and muffins tend to stick.
  • Filling the batter: You want to make sure all of the cupcakes are equal in size so that they bake evenly.
  • Other frostings: Healthy chocolate frosting, healthy cream cheese frosting or Greek yogurt frosting.


Serving: 1cupcake (no frosting) | Calories: 223kcal | Carbohydrates: 18g | Protein: 9g | Fat: 15g | Saturated Fat: 1g | Trans Fat: 1g | Cholesterol: 28mg | Sodium: 192mg | Fiber: 3g | Sugar: 13g
Course: Dessert
Cuisine: American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  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.

    1. Yes, it is for sweetening. What liquid sweetener can she eat? Brown rice syrup or date syrup would work too.

  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. I think that would make them more like muffins. These cupcakes are already more dense because of whole wheat flour.

    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.

    1. Perfect for Easter! I see so many Easter themed desserts and none of them are healthy…making these was a nice fresh change!

4.91 from 10 votes (5 ratings without comment)

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