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Healthy Pumpkin Pie Muffins Recipe

  • Author: Diana of
  • Prep Time: 10 mins
  • Cook Time: 20 mins
  • Total Time: 30 mins
  • Yield: 6 1x


These pumpkin muffins are delicious, pretty, and healthy, too. Well, they may be more on the healthy side if you skip the streusel. It’s up to you how healthy you want to be. πŸ˜‰ In lieu of pumpkin pie spice, I used a combination of a few different spices (cinnamon, ginger, nutmeg, and allspice), but feel free to reverse substitute.
*Vegetarian, Vegan options*


  • 1 cup whole wheat flour (or sub flour of choice)
  • 1 cup spelt flour (or sub flour of choice)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1/4 teaspoon salt
  • 1/4 teaspoon ground ginger
  • 1/8 teaspoon freshly ground nutmeg
  • dash allspice
  • 1 egg (or use vegan substitute, like a flaxseed egg – 1 tablespoon ground flaxseed mixed with 3 tablespoons water – let sit for about 10 minutes)
  • 1/2 cup sucanat (or sub brown sugar for a sweeter flavor)
  • 1 cup canned pumpkin
  • 1 single serving applesauce (or 1/2 cup), preferably no-sugar added
  • 1/4 cup milk (I used 2%) (or use vegan substitute, like soy, rice, hemp milk, etc.)
  • 3 tablespoons canola oil (or other oil of choice)
  • 1 teaspoon vanilla extract
  • streusel topping, see below
  • about 2 tablespoons pepitas (pumpkin seeds), raw

Streusel Ingredients (optional)

  • 1/4 cup old fashioned oats
  • 2 tablespoon butter, melted/softened (or sub vegan substitute, like Earth Balance)
  • 2 tablespoon brown sugar
  • 1 tablespoon flour of choice
  • 1/4 teaspoon cinnamon


  1. Pre-heat oven to 350 degrees F and prepare a 12 cup muffin tin with non-stick spray or muffin liners.
  2. Add whole wheat flour, spelt flour, baking powder, baking soda, cinnamon, salt, ginger, nutmeg, and allspice into a medium bowl and whisk together.
  3. In a large bowl, whisk to beat egg and sucanat together till combined.
  4. Whisk in pumpkin, applesauce, milk, canola oil, and vanilla extract.
  5. Pour dry ingredient mixture into the wet ingredient mixture, and stir gently just to combine – careful to not over-mix.
  6. Pour muffin batter into muffin tin cups – about 3/4 full each.
  7. If using streusel topping, in a small bowl, combine oats, butter, brown sugar, flour, and cinnamon and stir together. Evenly distribute no top of the muffins.
  8. Sprinkle pepitas on top of the muffins. Press pepitas (and streusel) lightly into muffins (if they’re sticking up too much).
  9. Bake for 16-20 minutes until centers set or a toothpick inserted in the center of a muffin comes out clean.
  10. Cool at least 10-15 minutes, or until safe to eat, before serving. Enjoy!

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