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 lunch box, but the great thing 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 complements the pumpkin spices in these cups.

Gluten-Free Flax Pumpkin Pie Cups
Yields 12-14 cups
Cuisine: Baking
  • ½ cup + 2 tablespoons ground flax
  • 6 tablespoons hot water
  • 1 cup all-purpose gluten-free flour
  • ¾ teaspoon xantham gum (optional)
  • 1 tablespoon baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon pumpkin spice seasoning
  • 1 tablespoon ground cinnamon
  • ½ teaspoon salt
  • 3 tablespoons brown sugar
  • 1 cup pumpkin puree
  • ½ cup honey
  • ½ cup Greek yogurt
  • ½ cup unsweetened applesauce
  • 1 teaspoon vanilla extract
Optional Topping:
  • 2 tablespoons orange zest, 1 tablespoon brown sugar, 1 teaspoon ground cinnamon
  1. Preheat the oven to 350F, and lightly coat muffin pans with cooking spray. Set aside.
  2. In a small bowl, mix 2 tablespoons of the flax with the water. Set aside.
  3. In a large mixing bowl, blend together the remaining ½ cup flax, the flour, xantham gum (if using), baking powder, baking soda, pumpkin spice, cinnamon, salt, and brown sugar.
  4. Add the pumpkin, honey, yogurt, and applesauce. Mix until a batter forms.
  5. Add the vanilla. Add the flax and water mixture, which should now have a gel-like consistency, and mix well again.
  6. Fill each muffin cup about three-quarters full.
  7. Optional topping: Mix together the orange zest, brown sugar, and cinnamon. Sprinkle the mixture evenly over all the cups.
  8. Bake for 30 to 35 minutes, until a toothpick comes out clean.
  9. Cool in pans for 5 to 8 minutes, then remove and cool for 10 minutes before enjoying!



  1. Christian says

    These look tasty. I am not gluten free so I make pumpkin muffins by adding one can of pumpkin to one spice cake mix. Stir the mix into the pumpkin and cook in the oven according to the directions. If you have a gluten free spice cake mix then it would super easy. Just thought I’d tell ya. :)

  2. 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..

  3. 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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