With just a handful of nutritious ingredients, these Healthy Pumpkin Muffins are a treat that we love to make and enjoy each fall for breakfast, snack time, or as a simple side dish for dinner. And it’s easy to adjust for allergies as needed!


Healthy Pumpkin Muffins

This easy muffin recipe is loaded with nutrients and the batter simple stirs together in a bowl or blender. Plus, the muffins bake up in just 14 minutes! We make a few batches of these muffins each fall when pumpkin fever is running high—and if I’m lucky, I get to stash some into the freezer for future days.

I love this recipe even more because you simply stir the ingredients together in a bowl—no fancy tools or a pile of bowls needed. It also tastes, great, is super easy, a great way to use up leftover pumpkin, and would be a great one to make with the kids if you like to have them in the kitchen with you.

We love to eat these plain, topped with a drizzle of honey, or even topped with a smear of cream cheese to transform them into pumpkin cupcakes. And you can make one simple adjustment to make them added-sugar-free as a baby muffin.

Ingredients You Need

To make this pumpkin recipe, you’ll need the following ingredients so you know what to have on hand or to pick up from the store.

ingredients in healthy pumpkin muffins on counter.

Step-by-Step Instructions

Here’s a look at how to make these simple Pumpkin Muffins. Scroll down to the bottom of this post for the full information.

how to make healthy pumpkin muffins in grid of four.
  1. Preheat oven and grease a mini muffin tin with nonstick spray. Gather all ingredients.
  2. Add all ingredients to a blender and blend well. OR add to a large bowl and whisk well to thoroughly combine the wet ingredients into the dry ingredients.
  3. Spoon the batter into muffin tins. (Be sure to grease the tin well with nonstick cooking spray. I find that to be better than using muffin liners, which may stick to the muffins.)
  4. Bake until golden brown and firm to the touch. Remove from the oven and let cool on a wire rack.

TIP: The muffins are done when they are set on top, have little cracks, and a cake tester inserted into the center comes out cleanly.

healthy pumpkin muffins on rack

Protein Muffins with Pumpkin

The nut butter and eggs in these muffins lends each one almost 3 grams of protein, which is pretty good for a little muffin. Each muffin also has a range of balanced nutrition which makes them a nice snack or meal component.

They are very moist and not too dense, which makes them a nice texture for toddlers who may struggle with the texture of bread.

TIP: Cut them into small cubes for younger toddlers as needed for easier chewing.

pumpkin muffins on plate

Can I make these Pumpkin Muffins nut-free?

You can use sunflower seed butter instead of the almond butter called for in the recipe, but know that there seems to be about a 50/50 chance that the finished muffins will turn green. If you do use sunflower seed butter, I would recommend omitting the baking soda to reduce the likelihood of this happening. (They’d still be safe to eat, they’re just a funny looking color!)

pumpkin muffins in storage bag for freezer

How to Store

You can store these Pumpkin Muffins in an airtight container or storage bag in the refrigerator for up to 3 days or in the freezer for up to 3 months. Thaw at room temperature or in the fridge. We like to let these cool fully and eat them at room temperature or chilled.

If freezing in a freezer bag, lay flat so the muffins are in one layer so they’re easy to remove from the bag one at a time—or thaw evenly if thawing the whole bag at once.

Best Tips for Success

  • To make this pumpkin muffin recipe nut-free, use sunflower seed butter and omit the baking soda.
  • To make egg-free, use a product like Just Eggs instead of something like flax eggs.
  • Serve chilled or at room temperature.
  • You can use pureed butternut squash instead of pumpkin puree.
  • Use canned or homemade pumpkin puree.
  • Add ¼ cup raisins, cranberries, or chocolate chips to the batter for extra flavor. Add extra pumpkin spice or even a little ground ginger if you like.
  • Eat these plain, topped with a drizzle of honey, or apple butter.
  • Let the almond butter sit at room temperature for at least 30 minutes to ensure it’s not too hard when it’s time to stir.
  • Use the same amount of applesauce in place of the maple syrup to make these added-sugar-free.

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I’d love to hear what you think of the recipe if you try it, so please comment below with your thoughts!

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healthy pumpkin muffins on bear plate

Healthy Pumpkin Mini Muffins

Use a gluten-free flour blend or whole wheat depending on what works best for your family. This recipe has very little flour—that is not a mistake. They bake up wonderfully, so have faith! Adapted from Against All Grain. 
4.99 from 169 votes
Prep Time 10 minutes
Cook Time 14 minutes
Total Time 24 minutes
Cuisine American
Course Muffins
Calories 175kcal
Servings 12  (Makes 24 mini muffins)



  • Preheat oven to 350 degrees F and grease a mini muffin tin with nonstick spray.
  • Add all ingredients to a medium bowl and stir for 30-60 seconds to thoroughly combine. Or use a blender and blend well.
  • Spoon the batter into muffin tins. It should be about 1 ½ tablespoons of batter in each one.
  • Bake 14 minutes, or until a toothpick comes out clean. Allow to cool in muffin pan. Remove and serve.



  • Store in an airtight container in the fridge for up to 5 days. Or freeze in a freezer bag with as much air removed as possible for up to 6 months. Serve warm or chilled.
  • Add ¼ cup raisins or chocolate chips to the batter for more flavor.
  • Nut-free: Use sunflower seed butter in place of the almond butter and omit the baking soda.
  • Gluten-free: Use cup for cup GF flour in place of the whole wheat flour.
  • Use canned or homemade pumpkin puree.
  • Serve chilled or at room temperature.
  • Eat these plain, topped with a drizzle of honey, or apple butter.
  • You can use honey instead of maple syrup if you prefer for kids over age 1.
  • Use ¼ cup applesauce in place of the maple syrup to make these added-sugar-free.


Serving: 2muffins, Calories: 175kcal, Carbohydrates: 11g, Protein: 5g, Fat: 13g, Saturated Fat: 1g, Polyunsaturated Fat: 3g, Monounsaturated Fat: 8g, Trans Fat: 1g, Cholesterol: 41mg, Sodium: 94mg, Potassium: 179mg, Fiber: 2g, Sugar: 5g, Vitamin A: 1649IU, Vitamin C: 1mg, Calcium: 103mg, Iron: 1mg
Tried this recipe?Rate in the comments and tag @yummytoddlerfood on IG!

This post was first published November 2017.

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How many stars would you give this recipe?


  1. 5 stars
    As someone who bakes frequently, I was worried about how this recipe would come out. Also, as someone who recently tried to give her toddler a healthy “cupcake” and failed, even more worried.
    But, honestly, I think this recipe is failproof. I substituted brown sugar for the syrup, as it was what I had on hand, and half of the oil with unsweetened applesauce. (Next time, I will only use the applesauce since the nut butter already has a decent fat content to it.) But, they came out perfectly. And my child LOVES them. I have no doubt that we will frequently be using this recipe. Thank you so much!

  2. Hello. So if using chia instead of eggs, do you grind them up first? Do you prefer chia over flaxmeal as an egg substitute for muffins? Thanks in advance 🙂

    1. When using chia, I don’t grind them first. Flaxseed meal can work too though I tend to use chia more often just as a preference.

    1. I haven’t tried that and haven’t combined the flavors of peanut butter and pumpkin but otherwise I’m sure that it would work fine!

  3. 5 stars
    Delicious, light and perfectly pumpkin spice-y. I made them with sunflower seed spread for my son’s school so they’d be nut free. Only downside is that the sunflower seed taste really came through but it was only an issue because it’s not my favorite taste. The kiddos didn’t mind though and it meant everyone was able to enjoy them. I will definitely make again at home with the almond butter.

  4. 5 stars
    I can’t truly rate the recipe yet, because I made a HUGE omission by mistake. Giving it a 5 star for my mistake version though. I forgot the almond butter. To my surprise, they came out amazing. Firm enough, but custurd-y. The flavor was great. I’ll have to try it with the almond butter next time, but for a lighter calorie mom-version of this snack, I’ll be cooking it without the almond butter again. (Feel free to use that omission as another recipe to post if you try and like it. Maybe “Gluten free Pumpkin Custard Bites” or something) I checked them after 12 minutes in the oven and took them on out. I subscribed to your email. I definitely need tips on feeding my 3 and 6 year old. We have gotten into some unhealthy food patterns and that needs to change.

    1. That’s so good to know! I have plenty of pumpkin but no almond butter in the house so your variation may happen this weekend!

  5. Thank you for this great recipe. Mine came out of the oven looking great…puffy, aromatic, delicious. But after I stored them in the refrigerator overnight in an airtight container, they turned GREEN! Has anyone else had this happen to their muffins? The flavor didn’t change, but I just found it strange that they turned green.

    1. Did you use almond butter or another nut butter? It’s possible the nut or seed butter interacted with the baking soda…though I’ve made these a few different ways and haven’t had that happen—but I know it sometimes can!

      1. Mine turned green too! I used sun butter. The color change didn’t affect flavor but I did find it odd. 🙂

      2. It seems to be a possibility with Sun butter but it doesn’t always happen. Odd for sure!

      3. I also used sun butter and topped with cream cheese frosting and I noticed some turned green where they interacted with the frosting. I didn’t refrigerate them, baked and brought right to an event.

      4. Thanks for sharing that! I’m trying to figure out a solution to still use Sunbutter but avoid the chance of the color issue.

  6. 5 stars
    Your muffins have become a staple at my house (applesauce, spinach/banana) and these are definitely in the rotation now! The flavor is great and the texture is really nice too- moist and fluffy. I followed the recipe exactly for the ingredients but did end up baking them a few extra minutes.

  7. These are so great! We used sunbutter instead of almond butter because of an allergy and they turned out wonderful. Thanks for the great recipe!

    1. I’d check them for doneness (a toothpick or cake tester comes out clean) starting at 18 minutes. It could take up to 22 or so.

  8. Thanks for the comment! It’s been a while since I’ve made these so I’ll plan to retest them this fall and will update the recipe if needed.

  9. Just to make sure before I make these with coconut flour.. Is it an even substitution of flour? Usually coconut flour is a small amount and I have been warned a little goes a long way. Thanks!! Can’t wait to try these

    1. Hi Faye. I haven’t tried these with coconut flour and I’ve only used it a few times so I don’t have a suggestion for a substitution other than start with less than the recipe calls for since it absorbs a lot and add more as needed to make a batter that looks like muffin batter should look. I hope you have success!

  10. Hi there! My son is allergic to eggs. Do you think yogurt is a good substitute in this recipe? I usually do a 1/4 cup for each egg in a recipe. Thanks!

    1. Hi! I haven’t used yogurt as an egg replacer before, but if you’ve used it in other muffin recipes, I would expect the results to be similar here. I have used chia seeds as an egg replacer in some muffin recipes with great success, so that would be an option too. Let me know if you have any other questions!

  11. Hi Amy!
    Made these last night. Only had 1/2 cup of almond butter but they still held up. Except mine turned out very dark and brown, not the pale orange of the ones in your photo. I was wondering if 1 1/2 TBSP of cinnamon is right? Maybe that’s why mine were so dark? Most recipes similar to this that I’ve made call for that amount but is tsp. any suggestions? Which brand of almond butter do you use? Regardless, they were tasty and my friends devoured them and wanted the recipe!

    1. Hi Anne! I did do tablespoons (the flavor helps to perk up the squash) but the color would depend on the color of the almond butter (I usually either use Marantha or Zinke Orchards), the color of your maple syrup, and the color of your pumpkin. It’s also possible that reducing the amount of the almond butter impacted the color too. Either way, I’m glad that they tasted good!

      1. 5 stars

        Thank you Amy! We usually use Marantha but it was one of those weeks when we ran out before our next Des Moines day and had to get Justin’s from HyVee. Our pumpkin was pretty orange (our own, not from the can). We’ll need to stock up on cinnamon if we make these often. 🙂