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These healthy pumpkin muffins with a cinnamon crumble topping are the perfect treat for any occasion. Whether you’re looking for a quick breakfast, a wholesome snack, or a delightful dessert, these muffins are sure to please. Kids and adults alike will love the warm, comforting flavors of fall.

Homemade pumpkin muffin with cinnamon crumble.
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There is no better way to roll in the cooler fall weather than baking all things pumpkin. I love that adding a healthy vegetable into everything is a fall tradition! Pumpkin muffins, pumpkin soups, or even my paleo pumpkin bread, count me in! 

My kids love to help in the kitchen, and between my applesauce muffins and this recipe, we always have a treat to bake!

With the added cinnamon crumb topping, they are my favorite pumpkin muffins. My kids love them too! Plus, they are gluten-free!

Why you will love this recipe

  • With minimal effort, you can whip up a batch of these tasty little muffins. They’re ideal for busy mornings or a satisfying afternoon snack.
  • These muffins are not only tasty but also packed with essential nutrients. They’re the perfect way to fuel your day, whether you’re on-the-go or enjoying a leisurely breakfast.
  • By baking with pumpkin, I can bring the warmth and coziness of fall into my own kitchen. It’s a simple way to elevate my baking and create delicious treats that truly capture the essence of the season.

Ingredients

Ingredients for the pumpkin muffins.

For the muffins

  • Coconut Flour (ยฝ cup): This gluten-free wonder helps our muffins rise beautifully and keeps things low-carb! It’s super absorbent, so make sure to measure carefully.
  • Almond Flour (ยผ cup): Another gluten-free friend! This flour adds a touch of protein and nutty flavor to our muffins.
  • Pumpkin Pie Spice (ยฝ tablespoon): This magical blend of warm spices (think cinnamon, nutmeg, ginger, and cloves) gives the muffins that classic fall flavor we all crave.
  • Baking Soda & Baking Powder (Dream Team!): These leavening agents work together to make your muffins light and fluffy.
  • Salt (ยผ teaspoon): A sprinkle of salt enhances all the other flavors in the muffins. Don’t skip it!
  • Coconut Sugar (โ…“ cup): Just like in the crumble, this natural sweetener adds a touch of caramel flavor that pairs perfectly with the pumpkin.
  • Eggs (4): These bind all our ingredients together and add richness to the muffins.
  • Pumpkin Puree (1 cup): The star of the show! This seasonal ingredient adds moisture, flavor, and that gorgeous orange color to our muffins. Be sure to use pure pumpkin puree, not pumpkin pie filling!
  • Vanilla Extract (1 teaspoon): A touch of vanilla extract rounds out all the other flavors in the muffins.
  • Coconut Oil (2 tablespoons): This healthy fat keeps our muffins moist and adds a touch of subtle coconut flavor. Feel free to substitute melted butter if you prefer.

For the cinnamon crumble

  • Almond Flour: This gluten-free superstar adds a delightful nutty flavor and texture to our crumble topping. I love the subtle sweetness it brings, too!
  • Coconut Sugar (โ…“ cup): This natural sweetener is the perfect partner for our crumble. It adds a touch of caramel flavor that takes things to the next level!
  • Cinnamon (1 tablespoon): We can’t resist the warm hug of cinnamon in this crumble! It complements the other flavors beautifully and makes your kitchen smell like fall heaven.
  • Solid Coconut Oil (ยผ cup): This healthy fat helps bind the crumble ingredients together and adds a subtle coconut taste. (Feel free to use melted butter if coconut isn’t your jam!)

Healthy pumpkin muffin recipe

Dry ingredients combined in a clear mixing bowl with a wooden spatula.

Step 1: Preheat oven to 375ยฐF. Mix all the dry ingredients for the muffins together in a small bowl.

Wet ingredients for the pumpkin muffins getting stirred in a clear mixing bowl with a metal spoon.

Step 2: Combine wet ingredients for the muffins in a separate mixing bowl.

Combining the wet and dry ingredients for the healthy pumpkin muffins in a large mixing bowl.

Step 3: Combine wet and dry ingredients and mix until well incorporated.

Crumble ingredients to top the muffins with are being combined in a small bowl.

Step 4: Add all the ingredients for the cinnamon crumble to a small bowl and mix well.

The muffin batter in a muffin tins with sleeves.

Step 5: Line a muffin tin with parchment paper muffin liners and fill with batter just below the top.

Pumpkin Crumble is spread on top of the muffins while they are still in the cookie tray.

Step 6: Sprinkle the cinnamon crumble on top of the batter. Bake in a preheated oven for 25 minutes or until a toothpick inserted in the middle of a muffin comes out clean.

Healthy pumpkin muffins on a light colored towel with a glass milk jar behind it and several more pumpkin muffins on a serving plate.

Expert Tips

  • You can grease the muffin tins with coconut oil, or you can use parchment paper muffin liners. I discovered the parchment paper muffin liners a few years ago, and I will never go back! They are the best!
  • Baking with gluten-free flour is similar to all-purpose flour, but it can be a bit denser. To achieve fluffy gluten-free muffins, be sure to add extra liquid to your recipe.
  • If you’re using coconut flour in your baking, you’ll notice that recipes often call for a larger amount of eggs. This is because coconut flour is highly absorbent and requires extra liquid to bind the ingredients together.
  • The pumpkin puree also adds a lot of liquid, keeping these muffins from getting dry. 
Several pumpkin muffins cooling on a wire cooling rack.

Recipe FAQs

Should I use canned pumpkins?

You can use either canned or fresh pumpkin puree for these healthy pumpkin muffins. If you use fresh pumpkins, be sure to stick to pie pumpkins.

How long will these last?

These muffins, stored in an airtight container, should last up to 5 days at room temperature or up to a week in the refrigerator.

Can I freeze these muffins?

If you want to make a double or triple batch, you can freeze them. Once they are completely cool, put them in a freezer-safe bag, and then place them in the freezer. If they are in a sealed bag or airtight container, they can last for 6 months in the freezer.

A healthy pumpkin muffin with a cinnamon sugar crumble sitting on a white table.

Related Recipes

If you tried this Healthy Pumpkin Muffin Recipe or any other tutorial on my website, please leave a ๐ŸŒŸ star rating and let me know how it went in the ๐Ÿ“ comments below. Thanks for visiting!

4.59 from 34 votes

Healthy Pumpkin Muffins with Cinnamon Crumble

Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
Servings: 12
Pumpkin muffins make the perfect fall breakfast or treat. This healthy pumpkin muffin recipe with cinnamon crumble is my favorite and definitely kid-approved.

Equipment

  • Mixing bowlย 
  • muffin tin
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Ingredients 

Cinnamon Crumble

  • ยฝ cup almond flour
  • โ…“ cup coconut sugar
  • 1 tablespoon cinnamon
  • ยผ cup solid coconut oil

Muffins

  • ยฝ cup coconut flour
  • ยผ cup almond flour
  • ยฝ tablespoon pumpkin pie spice
  • 1 teaspoon baking soda
  • ยฝ teaspoon baking powder
  • ยผ teaspoon salt
  • โ…“ cup coconut sugar
  • 4 eggs
  • 1 cup pumpkin puree
  • 1 teaspoon vanilla
  • 2 tablespoons coconut oil

Instructions 

Cinnamon Crumble

  • Mix all the dry ingredients together in a small bowl.
  • Using a fork, smash the solid coconut oil into the dry ingredients until well mixed.

Muffins

  • Preheat the oven to 375 degrees.
  • Add all ingredients into a large mixing bowl and whisk together until well combined.
  • Line a muffin tin with parchment paper muffin liners.
  • Fill the muffin liners almost to the top with the batter. (Leave a little room for the cinnamon crumble.)
  • Sprinkle the cinnamon crumble on top of the batter.
  • Bake in a preheated oven for 25 minutes or until a toothpick comes out clean.

Video

Notes

  • You can grease the muffin tins with coconut oil, or you can use parchment paper muffin liners. I discovered the parchment paper muffin liners a few years ago, and I will never go back! They are the best!
  • If your coconut oil is melted, place 1/4 cup in the freezer before making the crumble.
  • Place the cinnamon crumble in the freezer while making the muffins to keep the coconut oil from melting.
  • Be sure to check out the video tutorial above!

Nutrition

Calories: 141kcal, Carbohydrates: 15g, Protein: 4g, Fat: 8g, Saturated Fat: 3g, Polyunsaturated Fat: 0.3g, Monounsaturated Fat: 1g, Trans Fat: 0.01g, Cholesterol: 55mg, Sodium: 207mg, Potassium: 67mg, Fiber: 3g, Sugar: 7g, Vitamin A: 3259IU, Vitamin C: 1mg, Calcium: 46mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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About Laura

Welcome to Our Oily House, Iโ€™m so glad youโ€™re here! Explore DIY cleaners, homemade soaps, skincare and hair care recipes, fragrance-free solutions, and sustainable laundry tips for a naturally inspired home.

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4.59 from 34 votes (33 ratings without comment)

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19 Comments

  1. Beth says:

    5 stars
    Make these today, yummy! Next time I am going add walnuts!

    1. Laura says:

      Fantastic idea! Glad you enjoyed it!

  2. Alexandra says:

    Is it possible to make this using a loaf pan instead?

    1. Laura says:

      Yes, you will have to adjust baking time!

  3. Rula says:

    Could these be made with all almond flour and just leave out coconut flour?

    1. Laura says:

      Switching almond flour for coconut flour is not an even exchange so I would have to test ratios.