Applesauce Cupcakes Recipe

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Healthy applesauce cupcakes are coming your way! Made with a base of almond flour, brown rice flour, and coconut flour, these gluten-free cupcakes are so soft and delicious. No butter or oils, and naturally sweetened with maple syrup and applesauce – no refined sugar in the applesauce cake or the healthy frosting! A great dessert recipe to serve to adults and kids alike!

Applesauce cupcakes recipe

What makes a cupcake different than a muffin? The frosting!

Our base of cinnamon applesauce muffins gets topped with my healthy cream cheese frosting and crumbled freeze-dried apples – yum!

After writing a whole cookbook on healthy muffins, I think of myself as a bit of a muffin expert. The next level of muffins definitely leads to cupcakes!

My kids love when I make these, and I do too since they are filled with so much goodness I can feel good about.

Not your average cupcake, my friends.

What makes these healthier cupcakes?

We’re swapping out the traditional white ingredients (white flour, white sugar, butter, or vegetable oil) for better alternatives.

The mixture of almond flour, brown rice flour, and coconut flour works really well together to leave you with a fluffy cupcake base.

Maple syrup is my go-to sweetener for most baked goods, and it totally works here too! Applesauce lends to the sweetness and also leaves you with moist cupcakes.

Plus, we’re simply using less sweetener than you’d typically find in traditional cupcakes.

Want alternatives for any of those ingredients? Keep reading and you’ll find the substation list down below!

Simple ingredients for healthy applesauce cupcakes

• almond flour
• brown rice flour
• coconut flour
• baking powder
• sea salt
• cinnamon
• eggs
• maple syrup
• unsweetened applesauce
• almond milk
• vanilla extract
• healthy cream cheese frosting
• freeze-dried apples

How to make no refined sugar applesauce cupcakes

Scroll down to view the recipe card below for the full ingredients list, nutrition facts, and step-by-step instructions.

1. Preheat the oven to 350 degrees F. Prepare a muffin tin with cupcake liners, or use silicone muffin liners instead of paper liners.
2. In a large bowl add the eggs, applesauce, maple syrup, milk, and vanilla extract. Whisk the wet ingredients together fully.
3. Into the same bowl, add the almond flour, brown rice flour, coconut flour, baking powder, cinnamon, and sea salt. Using a whisk, mix the dry ingredients in fully, but do not overmix. Alternatively, you can use an electric mixer at medium speed here.
4. Divide batter between the prepared muffin pan. Bake for 24-26 minutes, or until you insert a toothpick into the center of a cupcake and it comes out clean, or with a dry crumb.
5. Remove and cool on a wire rack.
6. Once the cupcakes are fully cooled, use a piping bag and frost with the healthy cream cheese frosting. On the top of each cupcake sprinkle the crushed freeze-dried apples.

Watch me make applesauce cupcakes

The full how to video can be watched below, or on my YouTube channel!

Can you double this recipe?

Yes, and I highly suggest it! You can easily double the recipe and freeze extra.

Check out the storing section below for the best way to freeze and store leftover cupcakes.

How to store leftovers

To store leftover cupcakes, you’ll want to place them in an airtight container and place them in the fridge. Store for up to 5 days.

You can also freeze these cupcakes! Here’s how:

Place the cupcakes on a parchment paper-lined baking sheet. Place in the freezer and allow the cupcakes to fully freeze.

You can then transfer the cupcakes into a freezer-safe storage container, or a freezer storage bag. Be sure to label and date the container, and store it for up to 6 months.

To defrost, simply remove the desired number of cupcakes and place them on the counter to defrost. You can also defrost the cupcakes in the fridge.

Do not warm the cupcakes in the oven or microwave as that will melt the frosting.

Substitutions

Below you’ll find a list of substitutions that will work well in this delicious applesauce cupcakes recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Almond flour – For a nut-free flour choice, try a mixture of oat flour and brown rice flour. You can also substitute whole wheat flour for almond flour (and even all-purpose flour in a pinch!)

Brown rice flour – Try oat flour in place of the brown rice flour here.

Coconut flour – Try almond flour in place of the coconut flour, but double the amount used. Coconut flour absorbs a lot more liquid than any of the other flours, so to replace it, you will need to increase the amount of flour.

Cinnamon – Turn these cupcakes into applesauce spice cupcakes by using pumpkin pie spice in place of the cinnamon. Or in addition to the teaspoon of ground cinnamon for extra spice and flavor!

Eggs – Need a non-egg option? Try making a flax egg by mixing 2 tbsp flax meal with 6 tbsp water. Stir and let it sit for 5 minutes to gel, then use.

Maple syrup – Honey will work as an alternative. Watch the cupcakes as they bake though, and honey tends to brown baked goods more quickly than maple syrup. For a non-liquid sweetener try coconut sugar or brown sugar.

Unsweetened applesauce – Use homemade applesauce in place of store-bought. For a non-applesauce alternative try pear sauce (like apple sauce but made with pears!), or canned pumpkin puree.

Almond milk – Any milk option will work in place for the almond milk in this recipe.

Cinnamon – Try a pumpkin pie spice mix or apple pie spice mix in place (or in addition) of the cinnamon in the recipe.

More easy recipes you’ll love

• Healthy cream cheese frosting recipe without butter
• Low sugar carrot cake recipe with greek yogurt cream cheese frosting
• No sugar banana cake
• Gluten free blueberry coffee cake

If you try this applesauce muffin recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather