Gluten Free Flax Pumpkin Pie Cups

Do you love to bake in the fall…or just any time of year for that matter!? I do! The spices and wonderful scents that fill my kitchen are undeniably amazing.gluten free flax pumpkin pie cups

These Gluten Free Flax Pumpkin Pie Cups are moist and delicious and are the perfect treat to put in your child’s lunch box! They are like eating pumpkin pie without the heavy crust. This recipe is also gluten, egg and nut free.

Here at MOMables we do our best to give you ideas in your weekly meal plan that are perfect for the lunchbox…but the great thing is is that the recipes can be used for multiple meals!

gluten free flax pumpkin pie cupsFUN FACT: Flax is a great source of fiber, calcium, and magnesium. It has a nutty aroma which compliments the pumpkin spices in these cups.

Gluten Free Flax Pumpkin Pie Cups
Yields 12-14 cups
Cuisine: Baking
  • 1 cup of all-purpose gluten free flour
  • ¾ teaspoon of xantham gum (optional)
  • ½ cup of ground flax + an additional 2 TB
  • 6 tablespoons of hot water
  • 1 tablespoon of baking powder
  • ½ teaspoon of baking soda
  • 1 teaspoon of pumpkin spice seasoning
  • 1 tablespoon of ground cinnamon
  • ½ teaspoon of salt
  • 3 tablespoons of brown sugar
  • 1 cup of pumpkin puree
  • ½ cup of honey
  • ½ cup of Greek yogurt
  • ½ cup of unsweetened applesauce
  • 1 teaspoon of vanilla extract
Optional Topping:
  • 2 tabelspoons of orange zest, 1 tablespoon of brown sugar, 1 teaspoon of ground cinnamon
  1. Preheat oven to 350 degrees and lightly grease muffin pans with cooking spray, set aside.
  2. In a small bowl, mix 2 tablespoons of ground flax with 6 tablespoons of hot water. Set aside.
  3. In a large mixing bowl, blend together dry ingredients - 1 cup of flour, xantham gum, ½ cup of ground flax, baking powder, baking soda, salt, brown sugar, pumpkin spice, ground cinnamon.
  4. Add pumpkin, greek yogurt, honey, & applesauce. Mix until batter forms.
  5. Add vanilla extract. In a small bowl add the flax & water (it should now have a gel like consistency) and mix well again.
  6. Fill each muffin cavity approximately ¾ full.
  7. Optional topping: Mix together orange zest, brown sugar, and cinnamon. Divide evenly amongst cups, by sprinkling the tops of each with mixture.
  8. Bake for 30-35 minutes.
  9. Let cool in pans for 5-8 minutes then remove and let cool 10 minutes before enjoying!


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  1. Jane says

    Hi! Is there a good substitute for the flax or does this really make the muffins? There is a child in my son’s class with a severe nut/seed allergy so I have to be careful what goes into his lunch.

    • says

      Cathy, I haven’t made these paleo and this is definitely not a 1:1 substitution. I’m pretty sure Against all Grain has a paleo pumpkin muffin recipe..

  2. Michele says

    Made these today and all of my kids enjoyed them (ages 1, 4 &7). My only question is – Is the inside supposed to be a little sticky – like a pumpkin pie? I think I did everything correctly but wasn’t sure about the texture. The taste was certainly great! Thanks for the great snack!

    • says

      The gum is optional. It’s used in gluten free baking to help thicken and also hold the ingredients together. Some people don’t like to use it (it can be pricey) and some GF flours already have it in the mix (like Better Batter).

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