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. 
4.99 from 125 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. 5 stars
    Can i make these with apple sauce instead of pumpkin puree for an apple variety? I see you have an apple muffin recipe but i just love that this one has all the nutritious almond butter!! Ps- we already tried them with pumpkin and they are superb! Totally your next “spinach banana muffins”.

  2. 5 stars
    These have turned out perfectly both times I’ve made them. I added a few sugar free chocolate chips to each mini muffin. My 15 month old and husband can’t keep their hands off these!

  3. 5 stars
    I wouldn’t call these muffins per se but they are quite pleasant. I love that one of the main ingredients is almond butter and there is so little flour.

    I made these following the recipe (with the apple sauce instead of maple syrup substitution). They could use a little pinch of salt and I sort of wished they had some sweetness, but the 1/4 cup applesauce was not up for such a task. The texture is delightful – fluffy but holding together perfectly. They taste like bread – neither savory nor sweet. Therefore a perfect canvas for some butter and maple syrup. I like them even though it’s not quite what I anticipated.

  4. 5 stars
    I had to bake these muffins an extra 15 minutes. Also, don’t understand why
    they are are falling apart when separating
    them to dry. I always use a silicone mini
    muffin pan and never grease it. Should
    I spray the silicone muffin pan?
    Thanks for your advice.

  5. 5 stars
    Love this, my 15mo old ate them right away! After rejecting everything else I had lol.. My batch made 30 mini muffins. They don’t taste sweet like the ABC muffins but still good.

    I do want to note that if anyone was looking for a “mess free” muffin – I wouldn’t say these are it. They are soft and pancake-y so they stick to hands and little faces.

  6. 5 stars
    Very easy. Popped all ingredients in the blender and poured into the muffin tins. As the recipe says, they baked up puffy.

    I love this website. Found it when searching for purée recipes for my granddaughter and now it’s my go-to.

  7. 5 stars
    Amazing as always! I made a quadruple batch in order to use a whole can of pumpkin, and each pan turned out wonderfully. My son loves these. I love that he’s getting peanut butter AND pumpkin in each one. They freeze well and still taste great after being reheated in the microwave. They smell really good too.

  8. 5 stars
    So fluffy and delicious! I love the so slight nutty flavor from the almond butter. These work great with gluten free flour.

  9. Could I use regular flour for this? Or almond flour? I’d prefer to use what I have on hand, but don’t wanna waste a bunch of ingredients if it won’t work!

  10. 5 stars
    My 17 mo and 372 mo (31 year old husband LOLOL) loved these so much! They didn’t last more than 1.5 days!

    Doubled the recipe and made regular sized muffins since I don’t have mini muffin tins. They came out fluffy and delicious. Thanks Amy!

      1. 5 stars
        I’ve used high-iron baby oatmeal, which is essentially oat flour, and it came out perfectly. I will say that I find the texture is better using 1/2 rather than only 1/4 cup of the oat “flour” though.

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