NEW! Pumpkin Cookbook

Paleo Friendly Pumpkin Gingerbread Muffins

Extra spicy and super moist these paleo friendly pumpkin gingerbread muffins are a healthy treat for the holiday season!  Pumpkin spice, pumpkin puree and molasses give these muffins festive flavor and extra nutrition too. 

paleo friendly pumpkin gingerbread muffins


You know I’ll always be loyal to pumpkin, but that doesn’t mean I can’t combine it with the other flavors of the holiday season! Enter these paleo-friendly pumpkin gingerbread muffins. Extra moist and super spicy from the pumpkin spice and ginger, they’re a treat you’ll want to have on your counter to pair with your morning coffee all December long! I may or may not be considering a 3 third batch in two weeks!

What you’ll need for this recipe: 

  • almond flour
  • tapioca flour
  • blackstrap molasses
  • pumpkin puree
  • pumpkin pie spice
  • lemon
  • coconut oil
  • baking soda
  • coconut sugar

This was my first time using tapioca flour, and I’m really happy with the way that the texture turned out! Tapioca flour or starch as you’ll see it on labels, helps to thicken  baked goods and is derived from the pulp of the cassava root. It can replace cornstarch as a thickener for pies and sauces and aids in creating a crisp crust and chewy texture in baking.

paleo friendly pumpkin gingerbread muffins

The addition of the lemon juice into the batter of these paleo-friendly pumpkin gingerbread muffins offsets the spice with a little bit of tartness. Iced or left plain, you can’t go wrong!


What is Molasses and is it healthy?

Blackstrap molasses is a byproduct of sugar cane’s refining process. Sugar cane is mashed to create juice, and then boiled once to create cane syrup. A second boiling creates molasses. Blackstrap molasses has the lowest sugar content of any sugar cane product and is actually packed with vitamins and minerals like iron, calcium, magnesium, B6 and selenium. It’s also digested slower than other sweeteners making it an especially good option for people with diabetes. Known for giving gingerbread its distinctive taste, you may want to consider using it in other baked goods or it could even work in a glaze for chicken!

Don’t forget! If you’re in the mood for more pumpkin recipes this holiday season be sure to check out this recipe for gluten free pumpkin snowball cookies and even more in my Once Upon a Pumpkin cookbook available on Amazon now!


Paleo Friendly Pumpkin Gingerbread Muffins

  • Author: Maggie Michalczyk, RDN
  • Prep Time: 10 minutes
  • Cook Time: 16 minutes
  • Total Time: 26 minutes
  • Yield: 12 muffins 1x
  • Category: muffins
  • Method: bake


Simple to make and bursting with festive flavor, you’ll want to make a double batch of these muffins right from the start! The light layer of lemon icing adds sweetness that complements the spicy fresh taste.



  • 2 cups blanched almond flour
  • 6 tbsp tapioca flour
  • 1 egg, room temp
  • 1/2 cup pumpkin puree 
  • 1/4 cup unsweetened almond milk
  • 2 tsp fresh lemon juice
  • 1/4 cup coconut oil, melted
  • 6 tbsp organic coconut sugar**
  • 1/4 cup blackstrap molasses
  • 1 tsp pure vanilla extract
  • 3/4 tsp baking soda
  • 1 tbsp pumpkin pie spice 
  • 2 tsp cinnamon
  • 1 tsp ginger
  • 1/4 tsp allspice
  • 1/4 tsp  salt

Lemon icing:

  • 1/2 cup powdered sugar
  • 1 1/2 tsp pure maple syrup
  • 12 tsp lemon juice (add more if icing is still too thick)
  • 1/4 tsp pure vanilla extract
  • pumpkin seeds for sprinkling on top if desired


  1. Line a 12 cup muffin pan with cupcake liners and preheat the oven to 350 degrees F.
  2. Combine the dry ingredients in a mixing bowl, stir, and set aside.
  3. In a separate large bowl, whisk the eggs  with the pumpkin, almond milk, lemon juice, coconut sugar, and molasses until well combined. Add the melted coconut oil, vanilla, and whisk until smooth.
  4. With a wooden spoon or spatula, stir the dry ingredients into the wet gently until just combined and you don’t see any flour spots.
  5. Transfer batter to prepared muffin pan, filling about 3/4 full to make 12 muffins. Bake in the preheated oven for about 16 minutes.*
  6. Allow muffins to cool for 5 mins before transferring to wire racks to cool completely. While muffins cool, prepare the icing. Whisk together the icing ingredients in a medium bowl, and drizzle over the cooled muffins.

  7. Store leftovers at room temp, covered, for one day and in the refrigerator for up to 4 more days. Enjoy!


*I made this recipe a few times and the muffins didn’t rise very much! Don’t let that be an indication of doneness. They’ll come out a little smaller than regular muffins because of the flours used.

**You can sub brown sugar if you don’t have coconut sugar, however brown sugar is not considered paleo.




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paleo-friendly pumpkin gingerbread muffins

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