Healthy Pumpkin Muffins

The glittery streusel topping on these healthy pumpkin muffins adds the perfect crunch, and the moist interior is pumpkin-spiced heaven. Includes vegan variation!

Healthy pumpkin muffins

These healthy pumpkin muffins are pretty much the best fall use of a muffin wrapper that there is. (In our humble opinion, of course!) They’re perfectly moist, made with pumpkin puree and infused with pumpkin pie spice. Then there’s the streusel topping: oats and glittery turbinado sugar. It makes a sweet crunch in every bite. Even better? Each one is less than 200 calories. We served them to guests and they could not stop talking about them! Also, our son Larson was a 100% fan. It made us realize: it was time to share this recipe. (See the vegan pumpkin muffins variation below, too.)

Want another flavor? Our apple muffins and banana muffins have the same streusel topping!

Pumpkin muffins

What makes these healthy muffins?

We admit: healthy muffins is a bit of an oxymoron. Most muffins are just glorified cupcakes. RIght? So we’ve made it a goal to make some healthy muffin alternatives. We think muffins should be full of nutrient-filled ingredients, and easy on the stomach. They should be something you wouldn’t be embarrassed to feed your 2-year-old for breakfast or snack. But at the same time, they have to be sweet enough to be a bit of a treat. Trust us, we’ve made healthy muffins that are barely sweetened, and they don’t go over well!

These healthy pumpkin muffins are a result of that balance: they’re healthy-ish enough to be deemed healthy, but not so virtuous that you only want one bite. Here’s what makes these have a healthy spin.

  • Under 200 calories. Our main goal for these to be considered healthy was that they should be under 200 calories.
  • Just sweet enough. These babies have just enough sugar: and with the streusel topping, perhaps a little more than our normal muffin. The muffins themselves are sweetened with maple syrup, which gives a gentler sweetness than refined sugar.
  • Nutrient-dense ingredients. Along with butter and sugar, these muffins are balanced out with heart-healthy oats, apple sauce and nutritious pumpkin puree.
  • Vegan variation. Vegan doesn’t mean healthy. But if you’re looking for a plant based recipe, this one is easily made into vegan pumpkin muffins.
Healthy pumpkin muffins

Tips for how to make healthy pumpkin muffins

Did we convince you yet? These truly are one of our favorites of this fall baking season. (Except for this vegan pumpkin bread, of course!) As you go about making these muffins, here are a few tips on the process:

  • Pumpkin spice. In this recipe we used our pumpkin pie spice recipe, but of course you could use a store-bought version as well!
  • Turbinado sugar. Turbinado sugar is raw sugar. It has large crystals and a caramel-y flavor that’s a bit more complex than refined sugar, which is more processed. You’ll need to find turbinado sugar for the crunchy topping: other sugar just isn’t quite the same! It’s available at mainstream grocery stores. If you can’t find it, substitute brown sugar.
  • Maple syrup. The muffin interior is sweetened all with maple syrup. We used maple often in our desserts (and our cocktail recipes, interestingly enough!).
Healthy pumpkin muffins

How to store muffins

Last note on muffins before we get to the recipe. What’s the best way to store these healthy pumpkin muffins with struesel topping? It’s a great question, because the texture of the streusel can easily be lost depending on the storage method. Here’s our recommendation:

  • 1 day: To store for 1 day, leave the muffins on a cooling rack and cover with a clean, dry dish towel. This way, the crunchy streusel topping will stay in tact.
  • Up to 4 days: To store for up to 4 days, place a paper towel in the bottom of a sealed container, then place the muffins in and place a paper towel on top. The paper towels will absorb the moisture that rises to the top of the muffins, which will help to retain the crunchy topping.
  • Longer than 4 days: For any longer than 4 days, freeze these healthy pumpkin muffins in a sealable container and store up to 3 months.

Make them vegan!

This recipe is easily made into vegan pumpkin muffins! All you have to do is substitute coconut oil for butter. In the muffin batter, you’ll use melted coconut oil. In the streusel topping, room temperature coconut oil makes for the crumbly crunch.

Healthy pumpkin muffins

This healthy pumpkin muffins recipe is…

Vegetarian. For vegan, plant-based, and dairy-free, use coconut oil (see below).

Healthy pumpkin muffins

Healthy Pumpkin Muffins

1 Star2 Stars3 Stars4 Stars5 Stars (35 votes, average: 4.31 out of 5)

  • Author: Sonja Overhiser
  • Prep Time: 20 minutes
  • Cook Time: 30 minutes
  • Total Time: 50 minutes
  • Yield: 12 1x


The glittery streusel topping on these healthy pumpkin muffins adds the perfect crunch, and the moist interior is pumpkin-spiced heaven



  • 1 1/2 cups plus 2 tablespoons all-purpose flour, divided
  • 3/4 cup rolled oats, divided
  • 1 tablespoon plus 1 teaspoon Pumpkin Pie Spice, divided
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon kosher salt
  • 1 cup pumpkin puree
  • 1/2 cup maple syrup
  • 1/2 cup applesauce
  • 1/4 cup unsalted butter, melted (for vegan, use melted coconut oil)
  • 1 tablespoon vanilla extract
  • 1/4 cup turbinado sugar
  • 1/4 cup salted butter, cold and cut into small pieces (for vegan, use room temperature coconut oil)


  1. Preheat the oven to 350 degrees Fahrenheit. Add 12 muffin cups to a muffin tin.
  2. In a medium bowl, mix the 1 1/2 cups all-purpose flour, 1/2 cup rolled oats, and 1 tablespoon of the pumpkin pie spice with the baking powder, baking soda, and kosher salt.
  3. In another bowl, combine the pumpkin puree, maple syrup, applesauce, unsalted butter (melted), and vanilla.
  4. Mix the wet ingredients into the dry ingredients and stir until a smooth batter forms.
  5. In another medium bowl, add the remaining 1/4 cup rolled oats, 2 tablespoons flour, and 1 teaspoon pumpkin pie spice along with the turbinado sugar and salted butter (cut into small pieces). Cut the butter into the remaining ingredients using a pastry cutter or fork until a streusel topping forms.
  6. Divide the batter evenly into the muffin cups, then top with a thin layer of streusel.
  7. Bake for about 25 to 30 minutes, until a toothpick comes out clean. Allow to cool in the pan for 5 minutes, then remove the muffins and place them on a cooling rack.

  • Category: Muffin
  • Method: Baked
  • Cuisine: American

Keywords: Healthy Pumpkin Muffins, Pumpkin Muffins, Healthy Muffins

More muffin recipes

If you’re a muffin person (and we assume you are!), here are a few more muffin recipes we think you’ll enjoy:

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About the Authors

Sonja Overhiser

Cookbook Author and writer

Sonja Overhiser is author of Pretty Simple Cooking, named one of the best healthy cookbooks of 2018. She’s host of the food podcast Small Bites and founder of the food blog A Couple Cooks. Featured from the TODAY Show to Bon Appetit, Sonja seeks to inspire adventurous eating to make the world a better place one bite at a time.

Alex Overhiser

Cookbook Author and photographer

Alex Overhiser is an acclaimed food photographer and author based in Indianapolis. He’s host of the food podcast Small Bites and founder of the recipe website A Couple Cooks. Featured from the TODAY Show to Bon Appetit, Alex is author of Pretty Simple Cooking, named one of the best vegetarian cookbooks by Epicurious.


  • Reply
    Susan Oher
    October 6, 2019 at 7:25 pm

    Ugh – when I doubled the recipe in the clickable box that indicated 2x, the direction amounts didn’t double. I totally winged it and the muffins were just so so.
    Maybe it’s a glitch you can fix?

    • Reply
      Alex Overhiser
      October 6, 2019 at 8:26 pm

      Oh no! We’ll talk to the developers about this!

  • Reply
    Robin A Brewer
    November 12, 2019 at 8:29 pm

    In step 2 , it states 1 1/2 cups flour which I followed. As the muffins were cooking I knew there was an issue! Looking back into the ingredients it was 3 cups.

    • Reply
      Sonja Overhiser
      November 13, 2019 at 11:26 am

      Can you tell me where you are seeing 3 cups? I’m not sure I understand your question!

  • Reply
    Nirupama Chintamani
    November 23, 2019 at 2:21 pm

    Loved these muffins! They have just the right amount of sweetness and are not heavy. Perfect with a cup of coffee. Thank you for creating a healthy recipe!

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