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Healthy Sweet Potato Muffins with Chocolate Chips

Delicious AND HEALTHY Sweet Potato Muffins! These toddler and kid-approved muffins are naturally sweetened and made with whole grains; the perfect grab-n-go breakfast, lunch box side or snack. And they are meal prep friendly so you can always freeze them for later!

Healthy Sweet Potato Muffins

My family’s newest meal prep obsession: freezer-friendly sweet potato muffins!

I love a good meal prep recipe. Having healthy breakfast and snack options on hand, just makes life easier.

When I’m meal prepping for my family, I look for recipes that are 1) healthy 2) simple 3) delicious.

These healthy sweet potato muffins check all three boxes:

  1. Healthy: these muffins are made with wholesome, simple ingredients like eggs and whole wheat flour. Loaded with vitamin A and fiber thanks to a whole can of organic sweet potato puree and ground oats or oat flour. They’re also made with NO refined sugar; rather naturally sweetened with applesauce and maple syrup.
  2. Simple: Most sweet potato muffin recipes require you to peel, chop and roast sweet potatoes which will then be blended into the batter. While this is great in theory, I’ve found a good can of organic sweet potato puree does the job just as well without all the extra prep time. In fact, I feel in love with canned sweet potato, pumpkin and squash during my baby-food making days with my son. They’re magic. Open the can and you have an solid base to make homemade baby food, muffins, pancakes, oat balls and more! In the case of these healthy sweet potato muffins, your batter comes together in under 10 minutes, and you have muffins fresh out of the oven in 30 minutes.
  3. Delicious: just try them!

These healthy muffins are perfect for back-to-school season. An easy grab-n-go breakfast for those mornings you’re rushing out the door.

I personally love mine slightly warmed up and topped with drippy nut butter. These healthy muffins are also the perfect lunch box side for kids and grown ups alike.

Canned sweet potato is much easier to find on grocery store shelves during the fall months as well.

Healthy Sweet Potato Muffins

Tips + Tricks For Making Healthy Muffins

My #1 trick: this silicone muffin pan. Muffins pop right out and it makes clean-up a breeze {which let’s be honest, clean up is the worst part of meal prep}! You don’t have to pre-grease this silicone muffin pan either, I can’t tell you the number of times I forget to grease my pans. I also use this silicone muffin pan to make my Baked Egg Cups.

Double the recipe to build up your freezer-stash. I’m a huge advocate of doubling the recipe and hiding half away in the freezer for those busy weeks when meal prep isn’t feasible. I wrap groups of 4-6 muffins in aluminum foil and place them in a freezer bag to store in the freezer for up to 3 months.

*Note, when I’m making these for freezer meal prep I often add 1/2-1 c shredded carrots; shredded in a food processor. Not only is this a sneaky way to add more veggies, but it adds more moisture to the muffins so they don’t dry out in the freezer. You may need to cook the muffins a bit longer {5-10 additional minutes} when adding shredded carrots.

Substitute canned pumpkin or squash for sweet potato. The base of this recipe is VERY forgiving — which means you can play around with it! You can easily substitute canned pumpkin or butternut squash puree instead of the sweet potato puree! Making these healthy pumpkin muffins or squash muffins.

Customize to fit your family’s needs. I always make 1/2 a batch with chocolate chips, and 1/2 a batch without. We like to eat the muffins without chocolate chips for breakfast and save the muffins with chocolate chips for snacks.

healthy muffins for kids

The Recipe: Healthy Sweet Potato Muffins

5.0 from 2 reviews
Healthy Sweet Potato Muffins
Prep time
Cook time
Total time
Easy, healthy muffins, made with wholesome real food ingredients! We love keeping a stash in our freezer for on-the-go breakfasts and lunch box sides.
Recipe type: Breakfast, Snacks
Cuisine: Muffins
Serves: 12 muffins
  • Ingredients:
  • 1 can (15 oz) Organic Sweet Potato Puree
  • 1 cup Whole Wheat Flour
  • ½ cup Oat Flour {or ground rolled oats}
  • 2 Eggs
  • ½ cup Unsweetened Applesauce
  • 2 tablespoons Maple Syrup
  • 2 tablespoons Melted Coconut Oil
  • ¼ cup Unsweetened Almond Milk or Milk of Choice
  • 2 teaspoon Cinnamon
  • 1 teaspoon Baking Powder
  • Optional: ½ cup Dark Chocolate Chips
  • Optional: ½ -1 cup Shredded Carrots
  • Optional: 1 tablespoon Flax Meal
  • Optional: 1 scoop Collagen Peptides
  1. Preheat oven to 350 degrees.
  2. Add all ingredients to a large mixing bowl and mix well.
  3. Stir in optional chocolate chips. I personally like to put 6 muffins in the muffin tin without chocolate chips and then stir in chocolate chips for the remaining 6 muffins.
  4. Dividing batter evenly into the muffin tin.
  5. Bake for 25-30 minutes at 350 degrees. *Note, if you add ½ c - 1 c shredded carrots you may need to bake for an additional 5-8 minutes.
  6. Cool muffins and enjoy!
  7. If you plan to freeze the muffins make sure they cool completely before preparing them for the freezer.
*Store leftover, cooled muffins in the refrigerate for up to 1 week, or freeze for up to 3 months in the freezer.

Note, you do not need a food processor to make this recipe. But a food processor does come in handy if you need to grind oats in oat flour or add shredded carrots; but a high-speed blender works great as well.

Looking for more toddler-approved and kid-approved recipes? My 2-year old son, Brody, loves these Smoothie Popsicles, Spinach Banana Pancakes, and allergy-friendly Chocolate Tahini Energy Bites.

Pin these Healthy Sweet Potato Muffins for later

chocolate chip sweet potato muffins

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  1. A tasty healthy muffin. I ate one without nut butters suggested and one with. Both good, but the nut butter brings it up a notch! Yum!

    • Hi Lauren! I personally haven’t tried making it with another kind of flour, but I’m pretty sure using 1c oat flour + 1/2c almond flour or coconut flour would work just fine to make this recipe gluten free! I hope that helps! -Lindsey

  2. Hi Lindsay! You mentioned using canned sweet potato for making baby food. Do you have a post about making your own baby food? I have a 3 month old so we are not there yet but I would love to reference that when he does!

    • Hi Leah! Congrats on your babe and I hope you’re doing well mama! I don’t have a post specifically on making my own baby food, maybe I’ll share more about that this second time around. But we did a mix of baby-led weaning + homemade purees. Some great + easy starter options — frozen peas + carrots, thaw + puree, add avocado, or mixtures like canned pumpkin/sweet potato/squash alone or add carrots or maybe a little applesauce to sweeten. Super simple, I would make them in bulk and then freeze them in ‘cubes’ in silicon ice cube tray. Then pop a couple cubes out to thaw or heat up and add a little breastmilk if you want and there you go! I hope that helps! Lindsey