Healthy Pumpkin Muffins

By Maria Lichty

Updated September 18, 2025

Jump to RecipePin Recipe4.69139

Healthy Pumpkin Muffins – Easy, Moist, and Perfect for Fall

Pumpkin season hits and I immediately start baking (pumpkin chocolate chip bread, pumpkin cake, pumpkin snickerdoodles, and more). I also love making these Healthy Pumpkin Muffins, they have been a staple in our house for years. They’re perfectly spiced, super moist, and naturally sweetened—making them a win for both kids and adults.

I originally created this recipe because I wanted a muffin that felt like a true fall treat but still used feel-good ingredients. These muffins are packed with real pumpkin flavor, a hint of maple sweetness, and all the cozy spices you crave this time of year. They’re tender and soft with a beautifully spiced crumb—and if you sprinkle a little turbinado sugar on top before baking, you’ll get that irresistible sugary crunch that makes them feel extra special. Fall perfection!

You can easily stir in chocolate chips, chopped nuts, or dried fruit to make them your own. They freeze wonderfully, which makes them perfect for meal prep, lunchboxes, or grabbing on your way out the door. I especially love one warm out of the oven, simple, cozy, and so satisfying.

Ingredients (with Helpful Notes)

• White Whole Wheat Flour or Whole Wheat Flour: Either flour works well here. White whole wheat gives a lighter texture while still offering whole grain nutrition. Regular whole wheat is a bit heartier. If you don’t have whole wheat flour, you can use all-purpose flour. And if you need the muffins to be gluten-free, swap all-purpose gluten-free flour.
• Baking Soda: Essential for rise—make sure it’s fresh (check the expiration date!) for best results.
• Spices: (Cinnamon, Ginger, Nutmeg, Cloves) These warming spices bring classic fall flavor.
• Pumpkin Purée: Use canned 100% pure pumpkin, not pumpkin pie filling. It adds moisture and rich pumpkin flavor.
• Eggs: Help bind the muffins and give them structure. Room temp eggs incorporate more smoothly into the batter.
• Pure Maple Syrup: A natural sweetener that adds depth without refined sugar. Use pure syrup, not pancake syrup.
• Oil: Oil keeps the muffins moist and tender. You can use coconut oil or avocado oil. If you are using coconut oil, measure, melt, and let it cool slightly.
• Unsweetened Vanilla Almond Milk: Adds moisture to the muffins. You can use any milk you like—dairy or non-dairy both work.
• Pure Vanilla Extract: Adds warmth and enhances all the other flavors.
• Turbinado Sugar (optional, for topping): Adds a sweet, sparkly crunch on top. Totally optional, but gives them a nice bakery-style finish.

Breakfast/Brunch

Healthy Pumpkin Muffins

These Healthy Pumpkin Muffins are moist, naturally sweetened, and packed with warm fall spices. Made with wholesome ingredients, they’re a cozy, guilt-free treat you’ll want to bake all season long.

4.69 from 99 votes

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Prep Time 15 minutes mins

Cook Time 20 minutes mins

Total Time 35 minutes mins

Cuisine American

Servings 12 muffins

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Ingredients

  

1x2x3x

• 1 3/4 cups white whole wheat flour or whole wheat flour (can use all-purpose)
• 1 teaspoon baking soda
• 1 1/2 teaspoons ground cinnamon
• 1/2 teaspoon kosher salt
• 1/2 teaspoon ground ginger
• 1/4 teaspoon ground nutmeg
• 1/8 teaspoon ground cloves
• 1 cup pumpkin
• 2 large eggs, at room temperature
• 1/2 cup pure maple syrup
• 1/3 cup coconut oil, melted and slightly cooled (can use avocado oil)
• 1/4 cup unsweetened vanilla almond milk, at room temperature (or any milk)
• 1 1/2 teaspoons pure vanilla extract
• Turbinado sugar, for sprinkling on muffins, optional

Instructions

 

• Preheat oven to 350 degrees F. Line a 12-cup muffin pan with paper liners or grease the cups with nonstick cooking spray. Set aside.
• In a medium bowl, whisk together the flour, baking soda, cinnamon, salt, ginger, nutmeg, and cloves. Set aside.
  
• In a large bowl, combine the pumpkin, eggs, maple syrup, cooled coconut oil, milk, and vanilla extract. Stir until smooth.
  
• Add the dry ingredients to the wet ingredients and stir with a spatula until just combined. Don’t over mix.
  
• Pour the muffin batter evenly into the prepared muffin cups. Sprinkle the muffins with turbinado sugar, if using. Bake for 20-24 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  
• Let the muffins cool and enjoy!
  

Notes

How to Store the Muffins:

• At Room Temp: Store in an airtight container for up to 3 days.
• In the Fridge: Will last up to a week. Reheat in the microwave for 10–15 seconds to soften.
• In the Freezer: Let cool and freeze for up to 2 months. Thaw or pop in the microwave straight from frozen.

Nutrition

Calories: 163kcal, Carbohydrates: 22g, Protein: 3g, Fat: 7g, Saturated Fat: 5g, Cholesterol: 27mg, Sodium: 206mg, Potassium: 92mg, Fiber: 1g, Sugar: 8g, Vitamin A: 865IU, Vitamin C: 0.9mg, Calcium: 41mg, Iron: 0.6mg

Keywords healthy pumpkin muffins, pumpkin

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