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These delicious Healthy Pumpkin Muffins are made with whole wheat flour, and pumpkin puree, naturally sweetened with coconut sugar, and packed with plenty of warm fall spices. Great for breakfast, snack or add chocolate chips and make it dessert!

Side shot of pumpkin muffins stacked on each other.
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Moist, fluffy, flavorful Healthy Pumpkin Muffins will have you so excited for the fall season! They’re easy to make with the perfect blend of cozy spices, pumpkin purée, whole grains, and just the right amount of sweetness. We love to enjoy them for breakfast, but they also make a satisfying grab-n-go snack. Freeze an extra batch, so you can enjoy a quick treat any time you’re craving pumpkin!

Why you should make this recipe

  • Quick & easy: This recipe is an easy fall breakfast or snack that can be ready in less than 30 minutes!
  • Healthier: These are more nutritious than your average bakery muffin. The ingredients are simple and wholesome, yet join together for amazing texture and taste.
  • So much pumpkin flavor: You’ll need 1 1/2 cups of pumpkin puree, which packs major flavor and is a great way to use up leftover pumpkin puree!
  • Versatile recipe: If you want to mix things up, you can add chopped pecans or mini chocolate chips to the batter for a different flavor. See below for more mix-in ideas!
Bitten into healthy pumpkin muffin sitting on a paper liner.

Ingredients needed

This healthy pumpkin muffin recipe is made with better-for-you ingredients that you can feel good about eating. Here’s what you’ll need:

  • Whole wheat flour: All-purpose flour definitely works, but whole wheat flour provides a hearty boost of fiber and nutty flavor in these pumpkin muffins.
  • Baking soda: To help the muffins rise a bit while baking.
  • Spices: Stir in a wonderful mix of cozy fall spices from pumpkin pie spice.
  • Eggs: Two large eggs will give this tenderness and structure.
  • Coconut sugar: To perfectly sweeten each muffin! Use an equal amount of brown sugar, if preferred.
  • Coconut oil: Add in a little melted coconut oil for moisture.
  • Milk: Feel free to use any milk you’d like to give this additional moisture and give the batter the right consistency. We typically use unsweetened almond milk because it’s low in calories and fat, and is nondairy.
  • Pumpkin puree: Make homemade pumpkin puree or use store-bought, just be sure not to grab pumpkin pie filling. It has added sugar and spices that we do not need in this recipe.
Flour, pumpkin puree, spices, sugar, and oil divided into small bowls.

How to make this recipe

Making this pumpkin muffin recipe is very easy! Simply mix wet ingredients in one bowl and dry ingredients in another, combine the two, and pour into a muffin tin. Here’s the simple method:

  1. Prep: Preheat the oven to 400°F and lightly spray a muffin pan with cupcake liners.
  2. Combine dry ingredients: Use 2 bowls. In the first one, mix the dry ingredients, flour, baking soda, and spices.
  3. Mix wet ingredients: In the second one, whisk the eggs, coconut sugar, oil, milk, and pumpkin puree.
  4. Stir together liquid ingredients with dry ingredients: Pour the wet mixture over the flour mixture, and stir just until combined.
  1. Bake: Divide the batter among your cupcake liners. Bake for 14-16 minutes, or until a toothpick inserted in the center comes out mostly clean.
  2. Cool and enjoy: Allow the muffins to completely cool on a rack.
Healthy pumpkin muffins cooling on a wire rack.

Expert Tips

  • Individual spices: If you don’t have pumpkin pie spice available, or you’d just rather use individual spices, you can substitute the 2 tsp pumpkin pie spice for 1 tsp cinnamon, 1/2 tsp ginger, and 1/4 tsp each nutmeg and allspice. If you’re really short on spices, simply sub the pumpkin pie spice with cinnamon. Just know that your muffins won’t have that same spice flavor.
  • Use two bowls for mixing: For soft and tender muffins, be sure to mix the wet and dry ingredients in separate bowls. This will give your muffins the best texture.
  • Don’t over-mix ingredients: To keep these light and fluffy, don’t over-mix the wet ingredients with the dry mixture.
top view of pumpkin muffins on a napkin with some cinnamon sticks on the left side by the muffins

Frequently asked questions

How many calories are in a pumpkin muffin?

This particular recipe for pumpkin muffins has 190 calories per muffin, 24 grams of carbs, 4 grams of protein, and 10 grams of fat. See the recipe card for more nutrition information.

Is pumpkin puree the same as canned pumpkin?

Yes, just be sure to grab the can that has only pumpkin listed in the ingredients. We love Libby’s brand. You’ll find the canned pumpkin down the baking aisle near other canned fruit products.

How many cups in a 15-ounce can of pumpkin?

One 15-ounce can of pumpkin usually is about 1 1/2 cups, so you will need about one full can for this recipe.

Pumpkin muffins in paper liners.

Serving suggestions

We love these with a slather of butter, drizzle of almond butter, or a little jam but they’re fabulous on their own too! For a complete breakfast, pair them with a garden veggie frittata or a crustless quiche.

Mix-in ideas

Feel free to add up to about 1 cup of any mix-in to change up the flavor and texture!

  • chocolate chips, cinnamon chips, white chocolate chips, or peanut butter chips
  • nuts (pecans, walnuts, etc.)
  • raisins or dried cranberries
  • pumpkin seeds

Storage recommendations

  • To store leftovers: Cool completely on a wire rack. Store at room temperature for up to about 2 to 3 days in an airtight container. If you need to store them for a longer period of time, I’d recommend keeping them in the fridge or the freezer. You can microwave refrigerated muffins for about 10-15 seconds to make them taste like they are fresh out of the oven.
  • To freeze: Wrap each muffin in plastic wrap, then place them in a resealable freezer bag and freeze for up to 3 months. Label the bag with the date! Let the muffins thaw at room temperature or rewarm gently in the microwave to enjoy.
Pumpkin muffins stacked on top of each other.

More healthy pumpkin recipes

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5 from 1 vote

Healthy Pumpkin Muffins

By: Rena
Servings: 12 muffins
Prep: 8 minutes
Cook: 15 minutes
Total: 23 minutes
Side shot of pumpkin muffins over each other.
These delicious Healthy Pumpkin Muffins are made with whole wheat flour, and pumpkin puree, naturally sweetened with coconut sugar, and packed with plenty of warm fall spices. Great for breakfast, snack or add chocolate chips and make it dessert!

Ingredients

  • 1 3/4 cups whole wheat flour
  • 2/3 tsp baking soda
  • 2 tsp pumpkin pie spice
  • 2 large eggs
  • 2/3 cup coconut sugar
  • 1/2 cup melted coconut oil
  • 1/3 cup milk of choice
  • 1 1/2 cups pumpkin puree

Instructions

  • Preheat the oven to 400°F and lightly spray a muffin pan with cupcake liners.
  • Use 2 bowls. In the first one, mix the dry ingredients, flour, baking soda and spices.
  • In the second one, whisk the eggs, coconut sugar, oil, milk, and pumpkin puree.
  • Pour the wet mixture over the flour mixture, and stir just until combined.
  • Divide the batter among your cupcake liners. Bake for 14-16 minutes, or until a toothpick inserted in the center comes out mostly clean.
  • Allow the muffins to completely cool on a rack.

Notes

Storing: These will stay fresh, covered, at room temperature for up to 2 days, or in the refrigerator for up to 4 days. For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator, then bring to room temperature or warm up in the microwave if desired.

Nutrition

Serving: 1muffinCalories: 190kcalCarbohydrates: 24gProtein: 4gFat: 10gSaturated Fat: 8gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 0.003gCholesterol: 31mgSodium: 95mgPotassium: 151mgFiber: 3gSugar: 7gVitamin A: 4826IUVitamin C: 1mgCalcium: 29mgIron: 1mg

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

Additional Info

Course: Breakfast, Snack
Cuisine: American
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