Healthy Pumpkin Breakfast Muffins

Healthy Pumpkin Breakfast Muffins

These healthy pumpkin breakfast muffins, with just a few chocolate chips, are freezer-friendly, lightly sweet, and naturally gluten free. Make a double batch!

Healthy pumpkin breakfast muffins baked and on a wire rack.

Why a homemade (make-ahead) breakfast is the best thing ever

Whether or not breakfast is the most important meal of the day (I think that’s been debunked!), I believe in the power of a homemade breakfast. I always have a freezer stocked with portable-if-necessary homemade gluten free breakfasts, and even have a cookbook filled with some of my favorite recipes. 

The power of these breakfasts is in the comfort and kindness that it shows my children, whether they realize it or not. Not only do they have something they love to eat every morning that they want it, but they know that I’ve made it for them. 

I think of it like a subtle, gentle reminder that I’m here, and I’m supporting them as they go through what is often a rigorous day. Each year of my children’s school lives has been trying for each of them in its own way. 

My kids may not always be comforted by talking about how they feel (although they all 3, thankfully, do talk to me). And they may not even always be hungry for breakfast. On a very basic level, though, I believe that the knowledge that I’ve gone out of my way is a comfort. 

I rarely eat these breakfasts, since I’m lucky enough to work from home so I can squeeze in a meal for myself whenever I have the time. But maybe every once in a while I should have one since I’m a mother, not a martyr. ?

Healthy pumpkin breakfast muffin batter raw in muffin tin.

A super versatile recipe

This recipe for pumpkin breakfast muffins is based on our beloved recipe for banana oatmeal muffins, first published in 2015. Those muffins are packed with whole grains, don’t have much sugar, no added butter or oil, but still tons of satisfying flavor.

That recipe also spawned our recipe for healthy blueberry muffins, another family favorite. The original banana recipe has mashed ripe bananas for flavor and structure. The blueberry muffin recipe replaces the bananas with smooth applesauce, which has a neutral flavor in baking.

Now, we’re using canned pumpkin puree, one of the best ingredients of the fall, in place of the mashed bananas or applesauce. We’ve also scaled the recipe up a bit for more generous muffins, and added pumpkin pie spice for more seasonal flavor. These muffins are still made without any butter or oil, and little sugar. 

Healthy pumpkin breakfast muffins baked in muffin tin.

How to make these pumpkin breakfast muffins

In the original recipe for banana oatmeal muffins, all of the ingredients except for the chocolate chips are combined in a blender, and processed until smooth. This recipe could be made in a similar fashion as well. 

This time, though, we blend the old-fashioned rolled oats into a flour in a blender first and whisk in the baking powder, baking soda, salt, and pumpkin pie spice, with some chocolate chips mixed in. The wet ingredients (the pumpkin puree, sour cream, eggs, vanilla, and sugar) are blended until smooth, added to the dry ingredients, and mixed to combine. The batter is thick but very soft.

Baking with oats, which are appropriate in the U.S. for those on a gluten free diet, is a great way to get more whole grains. You do have to be careful, though, not to overprocess batter that contains oat flour, or your baked goods may turn out gummy and somewhat tough.

Grinding the oats into flour first, and blending the wet ingredients until very smooth afterward, ensures that the oats aren’t overprocessed. You can, of course, also use pre-ground oat flour, but I never buy that since it’s so much cheaper to grind my own. Plus, oat flour never needs to be superfinely ground.

Healthy pumpkin breakfast muffins on a plate with a bite taken.

Ingredients and substitutions

Oats/oat flour: Certified gluten free oats are safe on a gluten free diet. But if you’re avoiding oats, you should be able to use quinoa flakes in place of the oat flour. Please see my full discussion of how to replace oats in baking.

Dairy-free: Since there’s no butter in these muffins, the only dairy is the sour cream. It can be replaced with nondairy plain yogurt, strained of liquid until it reaches the consistency of Greek-style yogurt. You can also use plain Greek-style dairy yogurt in place of the sour cream. 

Egg-free: Since there are 3 full eggs in this recipe, I’m afraid I don’t believe that any egg replacement would work. So sorry!

Pumpkin pie spice: To make 1 teaspoon of pumpkin pie spice, combine 1/2 teaspoon ground cinnamon + 1/4 teaspoon ground ginger + pinch (1/8 teaspoon allspice), pinch (1/8 teaspoon) ground cloves + dash freshly ground nutmeg.

Chocolate chips: You can either leave out the chocolate chips entirely or replace them with another mix-in like dried cranberries or cinnamon chips. 

Sugars: I like to use granulated coconut palm sugar in this recipe. If you don’t have that specific sugar, you can replace it with the same amount, by weight, light brown sugar.

You might also be able to make these muffins with Truvia brown sugar replacement blend. Keep in mind that Truvia and similar sugar alternatives tend to be drying, so you might need to add a bit more moisture. Try adding more pumpkin puree by the teaspoonful until you reach the proper batter consistency (watch the how-to video for guidance).

Overhead image of Healthy pumpkin breakfast muffins in muffin tin and cooling on wire rack.


These healthy pumpkin breakfast muffins, with just a few chocolate chips, are freezer-friendly, lightly sweet, and naturally gluten free. Make a double batch!

Like this recipe?

Prep time: Cook time: Yield: 12 muffins


3 cups (300 g) certified gluten free old fashioned rolled oats (if you need to be GF)

2 teaspoons baking powder

1/2 teaspoon baking soda

1/4 teaspoon kosher salt

1 teaspoon pumpkin pie spice

5 ounces semi-sweet chocolate chips

12 ounces canned pure pumpkin puree

2/3 cup (150 g) sour cream, at room temperature

3 eggs (150 g, weighed out of shell) at room temperature

1 teaspoon pure vanilla extract

3/4 cup (120 g) coconut palm sugar


  • Preheat your oven to 350°F. Grease or line the wells of a standard 12-cup muffin tin and set it aside.

  • In a blender or food processor, place the oats and process until ground into a powder. Transfer the oat flour to a large mixing bowl, add the baking powder, baking soda, salt, and pumpkin pie spice, and whisk to combine well. Add about 4 of the 5 ounces of the chocolate chips, and whisk to distribute the chips throughout the dry ingredients. Set the bowl aside.

  • Into the same blender or food processor, add the pumpkin puree, sour cream, eggs, vanilla, and coconut palm sugar, and blend until very smooth. Transfer the wet mixture to the bowl of dry ingredients, and mix by hand until combined. Divide the batter evenly among the prepared wells of the muffin tin. The wells should be completely full. Shake the muffin tin back and forth to distribute the batter in an even layer in each well. Sprinkle the tops evenly with the remaining chips.

  • Place the muffin tin in the center of the preheated oven and bake for 20 minutes, or until the tops of the muffins spring back when pressed gently in the center. Remove from the oven and allow to cool in the tin for 10 minutes before transferring to a wire rack to cool completely. Serve immediately or wrap tightly in freezer-safe wrap and freeze. Defrost at room temperature before serving.


Comments are closed.

  • Patricia C King
    October 22, 2019 at 9:05 AM

    Nicole I made these muffins yesterday. They were delicious, however, when I went to remove them from the paper liners they stuck to the paper and most of the muffin stuck to the liner. I let them rest in the pan for ten minutes and then took them out and let them cool completely before eating. Any ideas why they stuck to the paper and wouldnt come out? Thanks so much! Patricia

    • Nicole Hunn
      October 22, 2019 at 10:22 AM

      Hi, Patricia, usually if you allow muffins or cupcakes to cool completely before peeling off the wrapper the baked goods will have shrunk away from the liner enough that they won’t stick. But not all cupcake liners are created equal, I’ve found, unfortunately. You need what are called “greaseproof” liners. I buy them online, and also have good luck with the “If You Care” brand liners, which is what you see in the photos and video of this post. The regular Reynolds liners you find in the grocery store will stick almost every time!

  • Patricia
    October 21, 2019 at 7:34 PM

    Nicole recipie says to freeze when cool! Would they be okay to eat the following day without freezing or do they dry to quickly? I made happy faces with the chocolate chips on top?

    • Nicole Hunn
      October 22, 2019 at 10:23 AM

      Haha no you can definitely keep them covered and store at room temperature for at least a second day and they should be absolutely fine!

  • Misty Christy
    October 20, 2019 at 9:19 PM

    Have you (or anyone else reading this) tried these as mini muffins?

    • Nicole Hunn
      October 21, 2019 at 7:57 AM

      I haven’t, no, Misty, but they’d be fine as minis. Just reduce the baking time, but I’m not 100% sure by how much since I’ve never tried it. I’d keep an eye on them starting around 13 minutes, just to be safe.

  • Julie L
    October 16, 2019 at 6:27 PM

    I’m making our second batch of these today using the rest of the canned pumpkin from Sunday and some leftover baked garnet yams from the other night. Efficiency that makes the children feel loved and grateful is the best! Thank you for our new favorite muffin!

    • Nicole Hunn
      October 17, 2019 at 7:56 AM

      I just made a fresh batch last night, too, Julie! And with something quite similar in mind (and at my children’s request). Thank you for the lovely note!!

  • Dana Schwartz
    October 15, 2019 at 7:07 PM

    I’m a huge fan of the healthy banana oat muffins, and these are perhaps even better!! Thanks for another winning recipe :)

    • Nicole Hunn
      October 16, 2019 at 8:40 AM

      That’s so great, Dana! It’s just a super versatile recipe, and so easy to throw together. Thanks for letting me know. :)

  • Diane Buzek
    October 14, 2019 at 8:17 PM

    Yum as usual! Do you think if I used dried diced apples instead of choc chips I would have to change anything? Would it still be 4 or 5 oz? None on top, just mixed in. Thank you :) diane

    • Nicole Hunn
      October 15, 2019 at 8:00 AM

      Hi, Diane, if you’d like to use freeze-dried apples, that might work. Just dried apples still have quite a bit of moisture, so I’m not sure how that would affect the result. And I’d actually measure by volume, not weight, since they’re so light and you’ll otherwise end up adding so many. Start with 1/2 cup, maybe?

  • Sherryl Ford
    October 14, 2019 at 6:32 PM

    What kind of flour do you use in your recipe. And where can I purchaze it.

    • Nicole Hunn
      October 15, 2019 at 7:58 AM

      Hi, Sherryl, there is no flour at the start of the recipe. You grind the rolled oats into a powder. It’s all in the instructions!

  • Sandy
    October 14, 2019 at 2:33 PM

    Just made these -they are delicious! I used raisins and cranberries instead of chocolate chips because I want them for breakfast. I also didn’t have enough sour cream so used what I had and finished the measurement with regular yogurt and they turned out perfectly anyway. Thank you Nicole for the recipe. It will be on my regular rotation!

    • Nicole Hunn
      October 14, 2019 at 4:40 PM

      I’m so glad, Sandy! It’s definitely a forgiving recipe, so I’m not entirely surprised that you were able to fudge the sour cream a bit. And my kids LOVE eating chocolate chips in a muffin for breakfast. Clearly your approach is more respectable. ?

  • Amanda
    October 13, 2019 at 10:42 PM

    Could I sub almond flour for the oat flour?

    • Nicole Hunn
      October 14, 2019 at 12:58 PM

      I’m afraid you can’t do that, no, Amanda. Please see the ingredients and substitutions section for how to replace the oat flour if you need to do that.

  • Terri Whitaker
    October 13, 2019 at 8:55 PM

    I made these this morning. They were delicious!

    • Nicole Hunn
      October 14, 2019 at 12:59 PM

      So glad, Terri!

  • Shelley
    October 13, 2019 at 12:35 PM

    So I ended up making these with 4oz dried cranberries in the muffins, and a sprinkle of mini chocolate chips on the top. They are really delicious! Thank you, Nicole, for another great recipe! ?

    • Nicole Hunn
      October 13, 2019 at 12:49 PM

      Sounds delicious, Shelley!!

  • Vanessa L
    October 13, 2019 at 12:33 PM

    Can pumpkin butter be used instead of pumpkin puree?

    • Nicole Hunn
      October 13, 2019 at 12:49 PM

      I’m afraid not, Vanessa. You need single-ingredient pumpkin puree for this recipe.

  • Abby
    October 13, 2019 at 10:55 AM

    Do you happen to know the calorie content on this fantastic looking recipe? Thanks!

    • Nicole Hunn
      October 13, 2019 at 11:03 AM

      I’m afraid I don’t have the manpower to provide nutrition information for my blog recipes, Abby. But I really like the calculator on Cronometer.com. I hope that helps!

  • Shelley
    October 13, 2019 at 10:29 AM

    Cinnamon chips are a thing?! ?. WHERE do I find these??? I’m not a big fan of chocolate chips in muffins (or pancakes…weird, I know!), but cinnamon chips would be divine! ?.
    I ‘m making a pumpkin pie today (Thanksgiving here in Canada) and never know what to do with the leftover pumpkin. These will be perfect!

    • Nicole Hunn
      October 13, 2019 at 10:32 AM

      Haha, Shelley, yes! Cinnamon chips are a thing. Hershey’s Kitchens makes the ones I have seen. By the label, they’re GF, but since you’re in Canada it might be different. Hopefully not!
      And Happy Thanksgiving!!

  • Carmen
    October 12, 2019 at 9:04 PM

    You know yoghurt is dairy, right?

    • Nicole Hunn
      October 13, 2019 at 8:50 AM

      I sure do! That’s why for dairy-free, I specify nondairy yogurt. That’s by definition dairy-free, or you’re buying the wrong thing!

  • Vivian Howard
    October 12, 2019 at 11:07 AM

    I usually have the GF Quick Oats on hand. Can they be used in place of the
    Old Fashioned Rolled Oats? Seems to me they could, but just checking!

    • Nicole Hunn
      October 13, 2019 at 8:48 AM

      Sure, Vivian, just measure by weight!

  • Shannon Powers
    October 12, 2019 at 12:31 AM

    I believe apple sauce would work as an egg replacement it is a 1/4 cup of apple sauce per egg!

    • Nicole Hunn
      October 13, 2019 at 8:48 AM

      I’m afraid I don’t feel confident about that substitution, Shannon, especially in a recipe with 3 whole eggs. Sorry!

  • Kathleen
    October 11, 2019 at 3:11 PM

    Hi! How much oat flour would blending the rolled oats make ? I have oat flour. Thank you!

    • Nicole Hunn
      October 11, 2019 at 3:52 PM

      Hi, Kathleen, I really recommend that you measure by weight, and you won’t have to do any conversions. For reference, 1 cup of oat flour weighs approximately 120 grams, so 300 grams is 2 1/2 cups. But if you have a scale, just use that!

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