Best Healthy Pumpkin Spice Muffins

Pumpkin Desserts & Baked Goods

These healthy pumpkin spice muffins are made with simple ingredients, packed with nutrition from siggi’s yogurt and full of pumpkin flavor! They are the perfect thing to bake up on a cozy fall weekend and freeze well too! 

This post was created in partnership with siggi’s. All opinions are my own and I appreciate your support.

best pumpkin spice yogurt

Pumpkin spice muffins are a perfect fall treat you’ll come back to again and again all fall long! This recipe for healthy pumpkin spice muffins is super easy and made with nutritious ingredients and not a lot of sugar. They get a lot of their fluffy, moistness from the siggi’s pumpkin spice skyr added to the batter, which is one of my favorite pumpkin spice products of all time

The pumpkin spice skyr, or icelandic yogurt, elevates the muffins and adds to their delicious texture. I love knowing that siggis yogurt is adding more protein per bite too! Baked goods in the fall are truly my weakness but I always strive to sneak in more nutrition by way of pumpkin and in this case, siggi’s yogurt! 

best pumpkin spice muffins

The pumpkin puree plus the siggi’s pumpkin yogurt (since it contains real pumpkin!) give these healthy pumpkin spice muffins a nice dose of vitamin A, which is great for eye health and immune function.

If you follow me on Instagram then you know I live for the time of the year when all of the pumpkin products start hitting store shelves. Siggi’s pumpkin spice yogurt most of all! It’s spiced just right and makes a good protein-rich snack any time of day.

I love siggi’s because their yogurt is truly unlike all the rest. High in protein and low in sugar and made with simple ingredients, it’s a fridge staple of mine no matter the season. I totally get that the dairy aisle can be super confusing and overwhelming because there are so many options out there, which is why you want to be informed on making the best choice for your health. Read all about that in this post on what to look for on a yogurt label

Besides eating it out of the container with a little bit of granola sprinkled on top, I love baking with it like in this muffin recipe. It adds more nutrition to baked goods and parfaits like this avocado key lime parfait made with siggis too! 

Ingredients for the Best Healthy Pumpkin Spice Muffins 

  • whole wheat pastry flour or white whole wheat flour
  • pumpkin puree 
  • siggi’s pumpkin & spice yogurt 
  • unsweetened vanilla almond milk
  • maple syrup 
  • coconut oil
  • 1 egg
  • pumpkin pie spice
  • cinnamon  
  • baking soda
  • ginger
  • nutmeg
  • vanilla extract
  • pumpkin seeds 
siggis pumpkin spice muffins

Best Healthy Pumpkin Spice Muffins

Maggie Michalczyk, RDN
These pumpkin spice muffins are little fluffy pillows of pumpkin goodness. Super moist and fluffy and full of that fall flavor we all know and love! 
Prep Time 7 minutes
Cook Time 22 minutes
Servings 12 muffins


  • 1 1/2 cups whole wheat pastry flour or white whole wheat flour
  • 1 cup pumpkin puree
  • 1 container siggi’s pumpkin & spice yogurt
  • 1/3 cup unsweetened vanilla almond milk
  • 1/4 cup maple syrup
  • 1 tbsp. coconut oil
  • 1 egg
  • 2 tsp. pumpkin pie spice
  • 1 tsp. cinnamon
  • 1 tsp. baking soda
  • 1/4 tsp. ginger
  • 1/8 tsp. nutmeg
  • 1 tsp. vanilla extract
  • 2 tbsp. pumpkin seeds


  • Preheat oven to 350 degrees F. Spray 12 cup muffin tin with nonstick cooking spray. 
  • In a medium bowl, whisk together flour, baking soda, pumpkin pie spice, cinnamon, ginger, nutmeg and cloves.
  • Mix pumpkin, maple syrup, egg, oil, vanilla, yogurt and milk together in a medium sized bowl.
  • Add wet ingredients to dry ingredients and mix until just combined. Top with pumpkin seeds if desired. 
  • Use a cookie scoop to divide batter evenly into muffin tin and bake for 22 minutes. Drizzle almond butter on top of warm muffins and enjoy! Store in the fridge for up to a week or freeze for up to 3 months. 

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siggis pumpkin and spice yogurt

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