Sweet potato muffins with pecan topping are perfect for autumn or winter mornings on-the-go. Made with flax seed and whole ingredients, they’re like having a healthy Thanksgiving side dish in portable muffin form.
As much as I like to hover over my hot cup of coffee and savor the morning, some days are a little more rushed than others. This recipe is great for days where you crave the soothing feeling of being wrapped up in a warm blanket lingering over a hot beverage, but in reality you have to get out the door quick. Take a couple of these wholesome treats with you for a boost of energy you’ll need to face the day.
What Makes These Sweet Potato Muffins Healthy
These aren’t your typical sugary bakery muffins. They’re packed with ingredients that actually give you energy and keep you satisfied. The ground flax seed adds omega-3s and fiber, which helps you feel full longer without that mid-morning crash. Sweet potatoes bring vitamin A, potassium, and natural sweetness so you don’t need as much added sugar.
I use honey instead of refined sugar, and the pecans add healthy fats and protein. You can even swap the oil for unsweetened applesauce if you want to cut calories. The best part? They taste like a treat but work as a legitimate breakfast. I’ve taken these on hikes, packed them for road trips, and eaten them as a pre-workout snack. They hold up.
About This Recipe
This recipe for Sweet Potato Muffins was sent to me from Mitch at the Beaufort Inn in South Carolina. He’s had a lot of practice making breakfast over the years, even before life as an Innkeeper. Sundays used to be his only day off and he would make something delicious in the morning for his daughter and a houseful of her friends. Lucky girls!
I’ve played around with this recipe over the years (we originally posted this in 2009), and I’ve tweaked it just a bit, adding pecans and omitting the cranberries. But I’ve saved those different variations for you in the notes below the recipe.
One of the things I love most about fall are the spices. Clove. Cinnamon. Nutmeg. Allspice. Ginger. They all seem to bring with them a feeling of comfort and warmth. These muffins have two of those spices, cinnamon and clove, plus that secret ingredient flax seed to help you feel full longer and give you some extra energy.
Sweet Potato Muffin Ingredients
Flax seed is the secret ingredient that makes these little muffins wholesome, hearty, filling and delicious. But don’t over indulge in too many muffins or you’ll experience what I call a flax-itive.
A snapshot of what you’ll need!
The complete list of ingredients with measurements is included in the recipe card at the bottom. This is to help with your shopping list.
- white flour
- ground flax seed
- honey
- baking soda
- baking powder
- ground cinnamon
- ground cloves
- vegetable oil
- sweet potatoes
- eggs
- chopped pecans
- turbinado sugar
If you can’t find ground flaxseed, you can buy it whole and grind it at home. Rather than a spice mill, I grind my flax seed in a small coffee mill grinder. It does the trick pretty good. After grinding the flax seed, add them to your flour and spice mixture and mix well. Next, beat the eggs in a separate bowl.
Add your eggs, oil, and honey to the flour/flax/spice bowl. This is going to get real thick, real fast. I don’t recommend using a mixer or beater, or else your muffins will fall flat. Instead just a fork will do, and just fold the batter together.
The honey combined with the flax seed makes this a thick and hearty stick-to-your-gut kind of muffin. No fluffy pastry here. This is a get outside and go hiking-climbing-fall-leaf-collecting-pumpkin-picking kind of breakfast. Eat your heart out Kashi.
Fold in the nuts and sweet potatoes. Do you feel like you’re making your own super food bar yet? The recipes I post are usually not the healthy kind. Bookmark this one for when you get into the thick of the holidays full of butter and sugar and crave a less guilt-ridden snack. Just remember, don’t over indulge.
Scoop the wholesome goodness into greased muffin pans. I like to add a little flour too. It makes them pop out really easy and creates a little crust on the edge. You can also use paper or foil muffin cups.
Let the sweet potato muffins cool on a wire rack and enjoy! Pack them with you for a hike, fall festival, or to just get you through the work week.
Tips for Making Moist Sweet Potato Muffins
- The key to moist muffins is not overmixing the batter. Once you add the wet ingredients to the dry, just fold everything together with a fork until combined. You’ll still see some flour streaks, and that’s fine. Overmixing develops the gluten and makes them dense and dry.
- Also, don’t overbake. Start checking at 25 minutes. The tops should spring back when you touch them, and a toothpick should come out with just a few moist crumbs. They’ll continue cooking a bit as they cool in the pan.
- Using freshly baked sweet potatoes instead of canned makes a huge difference in moisture and flavor. The texture is creamier and they don’t have that tinny taste some canned versions have.
Storing and Freezing Sweet Potato Muffins
These muffins keep well at room temperature in an airtight container for 3 to 4 days. If your kitchen is warm or humid, store them in the refrigerator for up to a week.
To freeze, let them cool completely, then wrap each muffin individually in plastic wrap and place them in a freezer bag. They’ll keep for up to 3 months. To reheat, unwrap and microwave for 30 to 45 seconds, or let them thaw overnight on the counter. I usually make a double batch and freeze half for busy mornings.
Common Questions About Sweet Potato Muffins
- Can I use canned sweet potato instead of fresh? You can, but fresh tastes better. If you use canned, make sure it’s plain sweet potato puree, not the sugary pie filling. Drain any excess liquid before measuring.
- Can I make these muffins ahead of time? Absolutely. They actually taste better the next day once the flavors have time to develop. Make them on Sunday and you’ve got breakfast sorted for the week.
- What can I substitute for flax seed? You can use wheat germ or just add an extra half cup of flour. The muffins won’t be as filling, but they’ll still taste good.
- Can I make these dairy-free? They already are! There’s no milk or butter in this recipe.
- Why are my sweet potato muffins dry? Usually from overbaking or overmixing the batter. Check them at 25 minutes and stop mixing as soon as the ingredients are just combined.
Sweet Potato Muffins
Yield:
12
Prep Time:
15 minutes
Cook Time:
30 minutes
Total Time:
45 minutes
Ingredients
- 2 cups white flour
- 1/2 cup ground flax seed
- 1/2 cup honey
- 1/4 tsp baking soda
- 2 tsp baking powder
- 1 Tbsp ground cinnamon
- 1/2 tsp ground cloves
- 1/2 cup oil
- 2 cups sweet potatoes, baked
- 2 eggs, beaten
- 1 1/2 cup chopped pecans (1/2 cup for topping)
- 2 Tbsp turbinado sugar (for topping)
Instructions
- Preheat oven to 375 degrees
- Wash 2 sweet potatoes and poke holes in skin with fork. Wrap the sweet potatoes in foil and bake for 45 minutes to an hour until soft.
- Using a wire whisk, mix dry ingredients (flour, baking soda, baking powder, ground flax seeed and spices) in large bowl.
- Beat eggs in a separate bowl. Blend honey and oil in with the eggs, then pour mixture into the bowl with flour.
- Scoop the baked sweet potato out of the skins and measure out two cups. Add the sweet potato and one cup of the pecans to batter (set aside the remaining half cup for topping) Fold the mixture together by hand using a large spoon or fork.
- Spoon muffin batter into greased muffin pan (or muffin cups). Sprinkle tops of muffins with remaining pecans and turbinado sugar and bake for 25 to 30 minutes until golden.
- Cool on a wire rack for 15 to 20 minutes, then serve!
Notes
I like to use pecans since it reminds me of a sweet potato casserole. But you could also use walnuts, or even add a cup of dried cranberries too.
If you’d like the muffins to be more sweet and dessert-like, replace the honey with 3/4 cup of sugar.
You can substitute apple sauce for the oil.
Nutrition Information:
Yield: 12
Serving Size: 1
Amount Per Serving:
Calories: 372Total Fat: 22gSaturated Fat: 2gTrans Fat: 0gUnsaturated Fat: 19gCholesterol: 31mgSodium: 134mgCarbohydrates: 41gFiber: 5gSugar: 17gProtein: 6g
Nutrition information provided is only an estimate.
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Originally published on Inn The Kitchen, 09/09/09. Updated November 2025 with new photos and content.
