These healthy sweet potato muffins are made with simple, wholesome ingredients and have a delicious cinnamon sugar topping. They’re moist, fluffy and super easy to make!

I love a good pumpkin muffin during the fall, but these sweet potato muffins might just be my new favorite fall muffin!

They’re made with whole wheat flour, coconut sugar, Greek yogurt, sweet potato puree and warming spices like cinnamon and ginger and are seriously so good. And don’t get me started on the cinnamon sugar topping… once baked it create a delicious, sweet crust on these muffins that is chef’s kiss!

Why You’ll Love These Muffins

• They taste like sweet potato pie in muffin form!
• From start to finish these muffins come together in 30 minutes!
• Perfect for meal prep and make for a great grab-and-go breakfast or snack.
• Can easily be customized with different mix-ins and substitutions.
• Packed with vitamins, minerals and fiber thanks to the sweet potato, Greek yogurt and whole wheat flour.

Ingredients Needed

• whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy bread that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour.
• baking powder & baking soda – leavening agents that help the muffins rise.
• cinnamon & ground ginger – spices that add warmth and flavor to the muffins.
• sea salt – enhances the overall flavor of the muffins.
• sweet potato – adds moisture, natural sweetness, nutrients and a unique flavor to these muffins. You can use mashed baked sweet potato or sweet potato puree. You can also use canned sweet potato puree, which can typically be found in the canned vegetables aisle of most grocery stores. Just make sure you pick up a can with sweet potato as the only ingredient! My favorite store-bought brand is Farmers Market organic sweet potato puree.
• eggs – acts as a binder and provides structure.
• coconut sugar – a less refined sugar that sweetens the muffins.
• greek yogurt – adds creaminess and moisture without the need for a ton of oil. Plus, it adds some protein to these muffins. I recommend full-fat Greek yogurt for the best results, but 2% Greek yogurt will also work.
• avocado oil or olive oil – helps keep these muffins super moist and fluffy!
• vanilla – enhances the flavor.
• topping – a mix of coconut sugar and cinnamon for a little extra sweetness and spice.

How to Make

Prep: Start by preheating your oven to 350°F. Prep a muffin tin by lining it with silicone or paper muffin liners to prevent sticking.

Combine: In a medium mixing bowl, combine the whole wheat pastry flour, baking powder, baking soda, cinnamon, ground ginger and sea salt. In a separate, large mixing bowl, whisk together the sweet potato, eggs, coconut sugar, Greek yogurt, oil and vanilla extract. Add the flour mixture to the wet ingredients. Stir until just combined, being careful not to over-mix. A few lumps are fine.

Make topping: In a small bowl, mix together the coconut sugar and cinnamon to create the topping for your muffins.

Bake: Scoop and divide the batter evenly among the muffin cups. Sprinkle each with the prepared coconut sugar-cinnamon topping. Place the muffin pan in the preheated oven and bake for 18-20 minutes. The muffins are done when a toothpick inserted into the center of a muffin comes out clean.

Cool: Remove the muffin tin from the oven and place it on a cooling rack. Once the muffins are cool enough to handle, transfer them from the muffin tin to a wire rack to cool completely.

Substitutions & Notes

Flour – If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.

Gluten-free – I didn’t test these muffins with a gluten-free flour mix but you should be able to swap a gluten-free all purpose blend for the flour in this recipe. My favorite is Bob’s Red Mill 1:1 Gluten-Free Flour.

Coconut sugar – If you don’t like coconut sugar or can’t find any, brown sugar or regular cane sugar will work as a substitute. I’m not sure how a liquid sweetener like maple syrup would work as a substitute so I wouldn’t recommend trying it as it could change the texture of these muffins.

Oil – Melted coconut oil or butter would work well as a substitute if that’s what you have on hand.

Dairy-free – If you need these muffins to be dairy-free you can swap the Greek yogurt with dairy-free yogurt.

Vegan – I haven’t tested these muffins with an egg substitute, so I’m not sure how they would turn out, but I bet flax eggs would work as a substitute. If you try it definitely let me know how they turn out in the comments below.

Mix-in’s – I love these muffins as is but if you want to add some texture you could mix in some chopped pecans or walnuts. Want a little extra sweetness? Add in chocolate chips or dried cranberries.

How to Cook Sweet Potato

There are many ways you can cook a sweet potato to make sweet potato 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. 

What to Serve With Sweet Potato Muffins

These sweet potato muffins are the perfect simple breakfast or afternoon snack. Here are some serving ideas:

Tips for the Perfect Muffins

• Don’t over-mix: One of the key steps to achieving fluffy, tender muffins is to avoid over-mixing the batter. Stir until just combined for the best texture.
• Use room temperature ingredients: Make sure ingredients like eggs and Greek yogurt are at room temperature before mixing. This will ensure a smoother batter and more even cooking.
• Quality ingredients: Using high-quality ingredients, especially the spices and sweet potato puree can make a noticeable difference in flavor.
• Test for doneness: Insert a toothpick into the center of a muffin to check if they’re done. If it comes out clean or with just a few crumbs, they’re ready to come out of the oven.
• Cool properly: Let the muffins cool in the muffin tin for a few minutes before transferring them to a wire rack to cool completely. This makes them easier to handle and can improve the texture. And you don’t want to let the muffins cool completely in the muffin tin because they could continue to bake as they’re sitting and dry out.
• Don’t skip the topping: Don’t skip the cinnamon-coconut sugar topping. It adds an extra layer of sweetness and texture that complements the muffin perfectly.
• Use silicone or paper liners: These make for easy removal and less mess. If you don’t have liners, make sure to thoroughly grease the muffin tins.

How to Store Leftovers

Fridge: Store the muffins in an airtight container in the fridge for up to 5 days.

Freezer: These muffins freeze well! Simply store them in a freezer-safe bag or container for up to 3 months.

More Muffin Recipes

More Sweet Potato Recipes

Check out all of the sweet potato recipes as well as the full collection of muffin recipes on EBF!