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 on bear plateHealthy 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’s super easy and would be a great one to make with the kids if you like to have them in the kitchen with you.

TIP: 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!

Ingredients You Need

To make this recipe, you’ll need the following ingredients.

TIP: These muffins are naturally dairy-free, can be made gluten-free, and contain only 2 grams of sugar per mini muffin.

how to make healthy pumpkin muffins step by stepStep-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.

  1. Preheat oven and grease a mini muffin tin with nonstick spray.
  2. Gather all ingredients.
  3. Add all ingredients to a blender and blend well. OR add to a medium bowl and stir well to thoroughly combine.
  4. Spoon the batter into muffin tins. Bake!

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 in storage bag for freezerWhat’s the best way to store these muffins?

You can store these Healthy Pumpkin Muffins in an airtight container or storage bag in the fridge 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.

TIP: 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.

mini healthy pumpkin muffin on plate with appleCan I make these Pumpkin Muffins nut-free?

You can use Sunbutter 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 Sunbutter, 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!)

Best Tips for Success

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.  
4.96 from 45 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
  • 3/4 cup almond butter
  • 1/4 cup maple syrup
  • 1/2 cup pumpkin puree
  • 3 tablespoons neutral oil
  • 1 teaspoon vanilla extract
  • 1/4 cup whole-wheat flour
  • 1 teaspoon cinnamon
  • 1/2 teaspoon pumpkin pie spice
  • 1 1/2 teaspoons baking powder
  • 1/4 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 3 days. Serve warm or chilled.


  • You can use pureed butternut squash instead of pumpkin.
  • Add ¼ cup raisins or chocolate chips to the batter for an extra treat.
  • Nut-free: Use Sunbutter 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.
  • Serve chilled or at room temperature.
  • Eat these plain, topped with a drizzle of honey, or apple butter.
  • You can top each muffin with cream cheese frosting for a healthy Pumpkin Cupcake.
  • Use canned unsweetened pumpkin puree, not pie filling.
  • You can use honey instead of maple syrup if you prefer.


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!

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How many stars would you give this recipe?


  1. Is it really just 1/4 c of flour? Mine came out almost more like an egg bite than a muffin. Still good.

    1. I would check that the baking soda is fresh and active. It’s possible that contributed to their texture. It’s a low amount of flour, but the structure comes from the egg and almond butter.

  2. 5 stars
    Incredibly fluffy! I skipped the maple syrup and used pumpkin jam instead of the pumpkin purée and it worked! 🙂

  3. 5 stars
    My toddler loves this recipe! She’s not picky… but definitely does NOT like some things I’ve made. However these she eats everyday for a snack. I’m always happy to sneak a few bites because they are delicious! I’ve subbed peanut butter instead of almond butter and it’s so tasty.

  4. what can I use instead of the maple syrup as I do not want any added sugar? apple sauce or something else? and what quantity, thanks!

  5. 5 stars
    Love these muffins! One question… in the nutrition section it says serving size is 2 muffins — is that regular size or mini? Thank you 🙂

  6. 5 stars
    I almost never comment on recipes but I just love this recipe so much. I have used ww flour, gf flour and coconut flour on different occasions. I’ve used various nut butters and sunflower butter and subbed puréed pumpkin for sweet potato. Each variation came out great and my 2 yo LOVES them. This is my go to muffin recipe.