Fluffy, moist, flavorful and perfectly sweetened, these sweet potato muffins are delicious, made with whole wheat flour, are lower in added sugar than traditional muffin recipes, and a wonderful veggie muffin to add to your breakfast or snack rotation!

A whole wheat sweet potato muffin on a table with more muffins on a cooling rack blurred in the background

Veggie muffins are frequent flyers in our house. Truly, if I do one thing on Sunday to prep food for the week, it is to throw a healthy homemade muffin recipe into the oven so that we have them on hand to grab for breakfast, snacks or to toss into a lunch box. They just make hectic mornings a touch smoother.

These easy sweet potato muffins are a perfect thing to add to our muffin rotation. Fluffy and moist, they are perfect for using up leftover cooked sweet potatoes and adding veggies to breakfast or snacks. Made with whole wheat flour, less added sugar than many muffin recipes and the perfect level of cozy spices, these muffins are wholesome and delicious. Making a hearty batch of 12, this recipe can be done (start to finish) in about 30 minutes. Vegetarian and nut-free, these sweet potato muffins can easily be made dairy-free or egg-free.

How to cook the sweet potato for these muffins

You can cook your sweet potato however you prefer or use sweet potatoes leftover from dinner. But if you want to cook sweet potatoes specifically for making these muffins, I have found these methods below bring out the natural sweetness in sweet potatoes the best.

  • Baking them whole in your oven. Super easy with minimal prep and the perfect cooked sweet potato. This method takes 45 minutes to an hour, but you can make them ahead of time and store the sweet potatoes in your fridge until you are ready to make these sweet potato muffins.
  • Cook sweet potatoes in your slow cooker. Another great method that is easy, hands off and perfect for prepping potatoes ahead of time.
  • Make your sweet potatoes in your Instant Pot. Perfect for if you want cooked sweet potatoes for these muffins NOW! This method takes about 30 minutes and is perfect for cooking sweet potatoes quickly.

Can I use canned sweet potato in this muffin recipe?

Canned and pureed sweet potato is one of my favorite time saving hacks in the kitchen. However, it is has a much thinner + wetter consistency than homemade cooked/mashed sweet potato and makes the muffins a bit too moist. If you really want to use the canned sweet potato puree, I would suggest reducing the amount of sweet potato to about 3/4 of a cup or reduce the applesauce to 1/3 cup to help balance the moisture level of these muffins.

Tips and tricks for the best muffins

Let them cool for a bit before enjoying. 

While warm muffins fresh from the oven are amazing, resist the urge to eat these sweet potato muffins right away. Let them cool for 10-15 minutes.

Why? Because baked goods are still cooking when they are removed from the oven. As they cool, these muffins will firm up and finish setting. Biting into one of these muffins might make you think they are soggy in the middle and need longer to bake, when they actually don’t.

Don’t over mix the batter. 

One of my favorite things about these sweet potato muffins is how fluffy they are. The key to that fluff is to mix the wet and dry ingredients together until JUST combined. Over mixing can lead to dense, flat muffins. Boooooo! No one wants that, so don’t over mix!

How to store these muffins

These muffins can hang out on your counter for a day, but if you plan to enjoy them over several days pop them in the fridge! Keeping them in an airtight container in your refrigerator will help to keep these moist muffins fresh longer and prevent molding.

Or, you can freeze them! I like to store them in a large freezer bag or freezer-safe large container. To defrost, I like to take them out of the freezer and leave them on the counter to thaw overnight. Or, you can warm a muffin in the microwave for about 20-30 seconds.

Suggested Adaptations

  • Make these sweet potato muffins dairy-free by using your favorite plant based yogurt. I like cashew or almond based yogurts.
  • Need egg-free? Use 2 “flax eggs” to replace the chicken eggs in this sweet potato muffin recipe.
  • Use butternut squash or pumpkin puree instead of sweet potato. Reduce to 3/4 cup if using canned, as canned tends to have more moisture than homemade.
  • Reduce sugar to 1/3 cup if you prefer a less sweet muffin.
  • Add in chopped nuts, chocolate chips, or raisins.

Other veggie muffin recipes…

Did you try these sweet potato muffins and now you’re hungry for more? 

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A sweet potato muffin cut in half to show the muffin's texture. The muffin is resting on the liner and is next to a cooling rack with more sweet potato muffins.
Fluffy Whole Wheat Sweet Potato Muffins on a rack
5 from 11 votes

Fluffy Whole Wheat Sweet Potato Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Breakfast
Fluffy, moist, flavorful and perfectly sweetened, these sweet potato muffins are delicious, made with whole wheat flour, are lower in added sugar than traditional muffin recipes, and a wonderful veggie muffin to add to your breakfast or snack rotation!


  • 1 cup cooked and mashed sweet potato, if subbing with canned sweet potato puree, reduce the amount of sweet potato to about 3/4 of a cup
  • cup unsweetened applesauce
  • ½ cup brown sugar, or coconut sugar for refined sugar free
  • ¼ cup avocado oil, or melted coconut oil
  • ½ cup plain Greek yogurt
  • 2 teaspoons vanilla extract
  • 2 large eggs, can replace with 2 flax eggs to make egg-free
  • 1 ⅓ cups whole wheat flour
  • 1 ½ teaspoons cinnamon
  • ¼ teaspoon nutmeg
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt


  • Preheat an oven to 375 ℉ and line a muffin tin with liners or grease them with extra oil to prevent sticking.
  • In a large mixing bowl, combine mashed sweet potato, applesauce, brown sugar, eggs, yogurt, vanilla, oil, in a medium bowl and whisk until smooth.
  • Add the flour, baking powder, baking soda, salt, cinnamon, and nutmeg. Stir together until well combined and batter has a smooth consistency. Do not over mix.
  • Pour batter into the prepared muffin pan.
  • Bake in the preheated oven for 20 minutes or until a toothpick inserted into the middle comes out clean.
  • Let cool in pan for 5 minutes before transferring to a wire cooling rack.
    Baked sweet potato muffins cooling on a wire rack.
  • Let cool completely and store in an air-tight container in fridge for up to 4 days or in the freezer for a month.
Serving: 1muffin, Calories: 158kcal, Carbohydrates: 23g, Protein: 4g, Fat: 6g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.003g, Cholesterol: 32mg, Sodium: 203mg, Potassium: 122mg, Fiber: 2g, Sugar: 11g, Vitamin A: 1629IU, Vitamin C: 0.4mg, Calcium: 54mg, Iron: 1mg