Fluffy Whole Wheat Sweet Potato Muffins
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!

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…
- Chocolate Muffins (with veggies!)
- Oatmeal Green Smoothie Muffins
- Oatmeal Chocolate Chip Zucchini Muffins
- Healthy & Wholesome Banana Zucchini Muffins
- Banana Carrot Muffins
- Healthy Morning Glory Muffins
Did you try these sweet potato muffins and now you’re hungry for more?
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Fluffy Whole Wheat Sweet Potato Muffins
Ingredients
- 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
- ⅔ 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
Instructions
- 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.
- Let cool completely and store in an air-tight container in fridge for up to 4 days or in the freezer for a month.
Can gluten free flour be substituted?
I haven’t tried them gluten free but I bet a cup-for-cup gluten free flour blend would work. I find that it typically is as “thirsty” as whole wheat flour. If you give it a go, let us know how they turn out!
Can you sub the egg and oil out?
Hi Mary! You can use 2 flax eggs in this recipe to replace the chicken eggs. I have not tested these muffins without oil, but I know many times, one can sub oil with applesauce in baking. So maybe try that!
Thank you so much!
Okay, you’ve really outdone yourself with these! They are sooo fluffy and have a ton of flavor! Used a 3/4 cup of pumpkin puree per your suggestion, half a mashed banana (didn’t have enough apple sauce) and added 1/8 tsp of ground clove. Really really good!
Love that you loved these as much as I do, Eva! Totally sipping on coffee and enjoying one as we speak!
Holy moly are these delicious!! The texture is PERFECT and the flavor is so good! The cinnamon and nutmeg go so well with the sweet potato and wheat flour. These will be gobbled up quickly! Thank you for another home run recipe!
I’m so pleased to hear you loved them, Debbie! I love those spices with sweet potato too.
Can honey, maple syrup, or date syrup be used to substitute the sugar? I can’t have sugar or sugar substitutes.
I haven’t tested these with a liquid sweetener like maple syrup, honey or date syrup. Since it would add extra moisture, I’d start by reducing the applesauce to 1/4 or 1/3 of a cup to balance it out. Again, I haven’t tested it like this, but maybe that helps. If you give it a go, please let us know how it turns out
I’m sorry if this is a silly question – but should the sweet potatoes be measured in dry cups or wet cups? I’ve always done applesauce in wet.
I would do wet.
These are my new favorite muffins. The sweet potato allows you to have less sugar while still tasting sweet. I added a bit more of the spices than called for but I reach for these from my freezer weekly. Yum!
So glad you are loving these, Meredith! I’m all for upping the warming spices to hit your personal preference!
My husband and I loved the sweet potato muffins, making the 2nd time with pumpkin and the 3rd time with squash. So easy to follow the recipe, subbing in Splenda brown sugar, monk fruit, or the product stevia w/maltodextrin following package directions.
I have been using whole wheat pastry flour in all my muffin baking for 5 years. I will use vanilla, plain yogurt. Because I play around with several ingredients I became intrigued with all of your muffins because they use the ingredients that I love especially the avocado oil. Apple pie spice is good to change up the flavorings. I use lemon yogurt in lemon bread which could be a muffin. I am curious if you have experimented with coffee flavoring. I thought perhaps it might be taste good in your chocolate zucchini muffins which we adore. They are scrumptious and very moist. We eat for dessert.
Have you puréed cottage cheese for muffins? Dill bread uses 1 cup cottage cheese. Would it be similar to using buttermilk? I may try it myself. This muffin definitely deserves a 5 rating. My grandkids love your muffins.
So glad you enjoyed these! And it is funny….I have JUST started experimenting with pureed cottage cheese in muffins. I love the added protein and the fluff they give muffins.
This muffin was so light and fluffy! The perfect way to get in those veggies! Added dairy free chocolate chips because you can’t go wrong with chocolate!
So happy you enjoyed them, Valerie! And I agree, chocolate makes just about every muffin better!
Hi Morel,
If I want to make 6 muffins, can I just reduce the ingredients by one half?
Anita
Hi Anita, that should work fine!