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.

Related Recipes

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

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. 
4.98 from 97 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)


  • 3 eggs
  • ¾ cup almond butter
  • ¼ cup maple syrup
  • ½ cup pumpkin puree
  • 3 tablespoons neutral oil (such as canola or avocado)
  • 1 teaspoon vanilla extract
  • ¼ cup whole-wheat flour
  • 1 teaspoon cinnamon
  • ½ teaspoon pumpkin pie spice
  • teaspoons baking powder
  • ¼ teaspoon baking soda


  • 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. Can these be made without almond butter or sunbutter? What could we use instead? Those allergies run in our family and we’re not ready to introduce nuts or seeds to our 10 month old.

  2. 5 stars
    These are so good! I was worried that they wouldn’t go over that well because they’re a bit lower in sugar, but both of my boys loved them. And so did I! Thanks for all the great healthy muffin recipes!

    1. 5 stars
      I actually did it twice. First attempt, I substituted almond butter with Greek Yoghurt ( I didn’t have any on hand) so it turned out to be more of a quiche. My second try, I followed as it is. I was worried about the amount of whole wheat flour but I just continued on. The muffins turned great! They were still moist and soft for 3 days considering I kept them in the fridge. My toddler like both.

  3. 5 stars
    This recipe is perfect! The muffins turned out moist and fluffy and so so tasty! My 11 month old loved them and so do I! I’ll certainly be baking these again and again. Reading the recipe I couldn’t believe so little flour was needed. But I believe that the almond butternis what keeps them so moist and delicious. Thank you for this recipe!

  4. 3/4 cup almond butter and only 1/4 cup flour? Is this a typo or am I missing something. I follow the exact recipe and the batter is very loose because of the 3 eggs and also has a big chunk of almond butter in the middle.

  5. 5 stars
    Made with spelt flour and peanut butter because that’s all I had. I was a bit skeptical 6the 1/4 cup and re-read the recipe and comments multiple times. I felt the batter was just to soft. I ended up adding a couple of teaspoons of extra flour just to make me feel better. They came out surprisingly fantastic if I do say so myself. The peanut butter taste was prominent and I’m sure almond butter would have been milder and allowed the pumpkin flavors to shine through but it was still very good.

  6. 5 stars
    I made these muffins with the following modifications. We don’t eat a lot of “butters” (peanut, sunflower, almond, etc) and all I had was peanut butter and didn’t want to use that. So instead I used plain Greek yogurt.
    I also didn’t have maple syrup and so I used honey.
    I thought I had pumpkin pie spice but it turns out I didn’t (why am I even baking at this point??) so I used my own measurements of cinnamon, nutmeg, clove, and ginger.
    At the last minute I added grated carrot.
    The batter seemed thin, which worried me and I added a bit more flour…but I was scared to add too much since I just wasn’t sure how it was going to cook up.

    They cooked up surprisingly well but definitely came out quite quichey in texture. They’re very moist and easy to eat. They did hold their shape well. My 11 month old seemed to like them a lot. I found them quite flavourful and would probably tone down some of the spices.

    Will make again. Thanks!

    1. Delicious, I used Nutzo instead because that’s what I like and I don’t think it changed the taste much

  7. 5 stars
    This is my go-to muffin recipe for my 14 month old. If you follow the instructions, these bake perfectly. I love that these are muffins that my daughter can snack on that are actually fairly low in carbs but high in protein and fat – exactly what my growing vegetarian kiddo needs in her diet! We’ll be making these for years to come. For younger kids, we halved the amount of maple syrup with great results. They were still slightly sweet and delicious.

  8. 5 stars
    This recipe is easy, fast and delicious! My 14 month old loved the muffins. They are so moist perfect for him to chew since he has no molars. Mini pumpkin muffins will be a tradition for years to come in our home. Thanks Amy!

  9. This looks like a great recipe to try for my 13 month old. I would like to add just a little oatmeal. Do you know how that would change the quantity of other ingredients?

    1. I think you could probably use it in place of the flour or do half oatmeal and half flour with good results.

    1. yes! They freeze really well. Store in a zip top freezer bag and freeze for up to 3 months. Thaw at room temperature or in the fridge.

  10. Is there an error in the recipe, like it should say 1 and 1/4 cups of flour? I added 1/4 c of flour only as listed and the muffins turned out very oily and eggy. I did use regular butter instead of almond butter, but I doubt that was the issue.

    1. There is not an error in the recipe—regular butter will not bake the same as almond butter in this recipe due to it being very low in gluten. It works very well as written!

    2. I Agree it seemed very oily , the eggy-ness didn’t bother me. Also I used sunflower butter in hopes to take to preschool snack and that’s all I could taste, I want to try w 1/4c of the sunflower butter and 1c pumpkin. I tasted no pumpkin.

    1. 5 stars
      I made them with peanut butter instead of almond butter and replaced oil with apple sauce (same amount in recipe) and they came out delicious! Fluffy and the right amount of balanced flavors. My 2 year old ate 3 before I could even stop him! they were a big hit with both of my toddlers (2 and 3.5).

  11. 5 stars
    These were so good my 2 1/2 year old immediately gobbled up two! I added two tablespoons of Hemp hearts also for some added texture.

    Can these be frozen also?

    1. I’m so glad and I love the hemp seeds add! You can freeze them once cooled. Add them to a zip top freezer bag and freeze for up to 3 months. Let thaw at room temp or in the fridge or briefly warm in the microwave.