These gluten-free sweet potato cupcakes are made with a combo of almond and oat flour, naturally sweetened and loaded with cinnamon flavor. They’re fluffy, moist and absolutely delicious especially when topped with cream cheese frosting.

These sweet potato cupcakes are the perfect fall treat! They’re moist, flavorful, and packed with all the best fall spices. Plus, they’re super easy to make. So what are you waiting for? Get baking!

There’s nothing like a warm, freshly-baked cupcake! And this sweet potato cupcake recipe is the perfect way to enjoy the fall season. Made with nutrient-rich sweet potatoes, these cupcakes are not only delicious but good for you, too!

Why You’ll Love These Cupcakes

• The sweet potato adds nutrients and replaces some of the oil in these cupcakes.
• They’re gluten-free, naturally sweetened and can easily be made dairy-free.
• The combo of fall flavors + cream cheese frosting = chef’s kiss!
• They’re great for meal prep and can be enjoyed for a snack or dessert all week long.

Sweet Potato in Baked Goods

Why am I adding a vegetable to my cupcakes? Well, for good reason of course! The mashed sweet potato helps to keep these cupcakes moist without a ton of oil!

Beyond that, they are high in fiber and a variety of important vitamins and minerals like beta-carotene, vitamin C and potassium. Studies have shown sweet potatoes positively impact gut, brain, eye and immune health. And some studies have shown that certain antioxidants in sweet potatoes may protect against certain cancers. (Source)

Ingredients Needed

• sweet potato – you’ll basically be making sweet potato puree for this recipe. See below for a variety of ways that you can cook and puree your sweet potato. For a shortcut you can use canned sweet potato puree instead.
• unsweetened almond milk – I like using unsweetened almond milk, but feel free to use your favorite non-dairy milk or dairy milk. And make sure your milk is at room temperature, otherwise if it’s too cold it could cause the coconut oil to harden and clump up.
• eggs – helps bind the ingredients together. Also, make sure you’re using eggs at room temperature!
• maple syrup – my go-to natural sweetener of choice for these cupcakes. Make sure you’re using pure maple syrup and not pancake syrup, which is loaded with corn syrup!
• melted coconut oil – we’re just using a little oil in this recipe to keep the cupcakes extra moist and prevent the liners from sticking to the cupcakes.
• vanilla extract – a flavor enhancer. 
• oat flour – use store-bought oat flour or you can make your own using my oat flour recipe. If you’re making your own oat flour, about 1 1/4 cups rolled oats blended will yield 1 cup oat flour.
• almond flour – the combination of oat and almond flour make for a slightly nutty and dense cupcake. I recommend Bob’s Red Mill super fine almond flour as it’s perfect for baked goods.
• cinnamon – an essential spice for these sweet potato cupcakes.
• baking powder & baking soda – to help the cupcakes rise.
• sea salt – brings all the flavors together.
• cream cheese frosting – this is optional, but the frosting is definitely what takes these cupcakes to the next level! To make the frosting we’re whisking together cream cheese, Greek yogurt, maple syrup and vanilla extract. The tang of the cream cheese pairs perfectly with the sweet potato flavor and spice from the cinnamon!

Substitutions & Notes

• Vegan: I haven’t tried a vegan version of this recipe yet, so I’m not sure how they’d turn out, but if you decide to try these cupcakes with an egg substitute like flax eggs let me know in the comments below! And for the frosting, you can skip it altogether or use dairy-free cream cheese and yogurt.
• Dairy-free: To make this recipe dairy-free, skip the frosting or use a dairy-free frosting!
• Flour: I haven’t tried another flour for these cupcakes, so I’m not sure how they would turn out, but I would imagine using all-purpose flour would work if you don’t need a gluten-free flour option.
• Maple syrup: Any other liquid sweetener will work just fine like agave syrup or honey. To lower the sugar content of these cupcakes you could use monk fruit maple syrup.
• Sweet potato: You could try different variations of this recipe by swapping out the sweet potato with a pumpkin puree or butternut squash puree. These both have similar textures to sweet potato.
• Frosting: I personally love the addition of frosting with these cupcakes, but you could totally skip the frosting altogether or swap it out with your favorite frosting. This healthy chocolate frosting would pair nicely with the flavor of these cupcakes or you could try this creamy Greek yogurt frosting made with nut butter for a healthier alternative to the cream cheese frosting. If you don’t love cream cheese, you can try my vanilla buttercream frosting. If you’re going the store-bought route, my favorite brand is the Simple Mills vanilla frosting.
• Mix-ins: Feel free to add some of your favorite mix-ins to the recipe. Chocolate chips, dried fruit or nuts would all be delicious additions to this cupcake recipe!

How to Make

Begin by preheating your oven to 350°F and line a muffin pan with silicone muffin liners or paper muffin liners or spray tray with a cooking spray.

Whisk together the mashed sweet potato, milk, eggs, maple syrup, oil and vanilla extract in a large mixing bowl. Combine the flour, cinnamon, baking powder, baking soda and salt in a medium mixing bowl.

Add the dry ingredients to the wet ingredients and mix together, until just combined. Divide the batter evenly between the muffin cups and bake for 17-20 minutes, or until a toothpick inserted into a cupcake comes out clean. 

Let the cupcakes cool for a few minutes when you remove them from the oven. After a few minutes make sure to take them out of the muffin tin so they don’t continue to cook. Place the cupcakes on a cooling rack and begin to prepare your frosting. 

To make the frosting add all the ingredients to a medium mixing bowl and use a hand mixer on medium speed to whip everything together until smooth and fluffy, scraping down the sides as needed. When the cupcakes are cool, frost and enjoy!

How to Cook Sweet Potato

There are many ways you can cook a sweet potato to make puree! Here are my go-to methods:

Bake

Start by washing your sweet potatoes well. Use a fork to poke several holes in each potato – I usually poke 4 times for each potato! Place the potatoes directly on a baking sheet and bake at 400ºF for 60 minutes. Some people like to wrap their potatoes in aluminum foil but that actually steams the potato so just pop them right in the oven! You’ll know the potatoes are ready when they’re a little wrinkly and can easily be pierced with a fork. 

Steam

I’ve used this method for making pureed sweet potatoes for Olivia. It’s a bit faster since you’re chopping the sweet potatoes into small chunks. To steam, simply peel the sweet potato, cut into cubes, about 1 inch in size and steam. Add about 1-2 inches of water to pot, place the steamer basket in and add sweet potato cubes. Boil water, cover and let the sweet potatoes steam until soft. 

Boil

Boiling is another quick option. Simply peel the sweet potato and cut into cubes, about 1 inch in size. Bring a pot of water to a boil and add sweet potato chunks. Reduce to a simmer and cook until tender, around 15 minutes.

How to Puree Sweet Potato

After your sweet potatoes are fully cooked set them aside to cool. Once you can hold/touch without burning yourself, use your hands to peel the skin away from the flesh if you haven’t peeled them already. You can toss the skin or snack on it if you want – it’s loaded with nutrients!

When it comes to pureeing the sweet potatoes I usually use my food processor or Vitamix blender, but you can also use an immersion blender, potato masher or even a fork. 

Food processor – Add the cooked potatoes to your food processor and blend until smooth. 

Blender – Add the cooked potatoes to a high-powered blender and blend until smooth. 

Immersion blender – Add the cooked potatoes to a large bowl or pot and blend until smooth.

What to Serve with Sweet Potato Cupcakes

These cupcakes are delicious for an afternoon snack, dessert or even breakfast (especially if unfrosted) Here are some serving ideas:

• On their own with butter, coconut oil or nut butter spread on them paired with a warm pumpkin spice latte.
• Pair with hard boiled eggs, egg white bites or a breakfast wrap for a healthy breakfast on the go!
• Serve with spinach quiche, fruit salad and a mimosa for a fun brunch.
• Pair with any protein-packed snack for an afternoon pick-me-up.
• Serve with frosting for a healthy after dinner dessert.

How to Store Leftovers

I recommend storing these sweet potato cupcakes in an airtight sealed container in the refrigerator for up to one week. I haven’t tried to freeze any, but if you do, you should store them in an airtight container and they should be good for up to three months. 

More Sweet Potato Recipes

• Sweet Potato Baked Oatmeal
• Sweet Potato Breakfast Cookies
• Healthy Sweet Potato Casserole
• Sweet Potato Hummus
• Sweet Potato Nachos
• Sweet Potato Smoothie
• Healthy Sweet Potato Pie
• Dessert Baked Sweet Potato
• Sweet Potato Muffins

More Cupcake & Cake Recipes

• Healthy Vanilla Cupcakes
• Healthy Chocolate Cupcakes
• Almond Flour Cupcakes
• Healthy Vanilla Cake
• Pumpkin Coffee Cake
• Healthy Birthday Cake
• Apple Cake
• Easy Strawberry Cake
• Healthy Carrot Cake Bars

Be sure to check out all the sweet potato recipes as well as the full collection of dessert recipes on EBF!