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low fodmap pumpkin zucchini muffins on a cooling rack on a white painted background

Low FODMAP Pumpkin Zucchini Muffins (Gluten-Free)

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  • Author: Gail Gromaski
  • Total Time: 40 minutes
  • Yield: 12 muffins 1x
  • Diet: Gluten Free


These moist and delicious low FODMAP* Pumpkin Zucchini Muffins topped with a mouth-watering streusel are a great way to use up that zucchini from your garden (or your neighbor) while incorporating some classic fall flavors. Low FODMAP, gluten-free, dairy-free, and refined sugar-free.

*Please note: this recipe is under revision due to Monash University's recent testing of brown rice flour, found to contain moderate amounts of fructans. Pumpkin and zucchini also contain fructans. If you are able to tolerate brown rice flour or fructans, this may not be an issue for you.


Units Scale

Low FODMAP Streusel Topping (Optional)*

Dry Ingredients

Wet Ingredients 

  • 1 cup canned pumpkin puree*
  • 3 large eggs, at room temperature
  • 1 teaspoon pure vanilla extract
  • 1 teaspoon apple cider vinegar
  • 1/2 cup coconut oil, melted and just above room temperature
  • 2 cups zucchini, coarsely grated (about 1 medium)*


  1. {Optional} Prepare your streusel ingredients: About 1/2 hour prior to baking, stick 1/2 cup of solid coconut oil in the refrigerator to chill.
  2. {Optional} Make streusel topping: In a small bowl, mix streusel ingredients together with a fork or pastry knife until dime-sized chunks form. Cover and chill in the refrigerator until ready to use.
  3. Prepare your muffin ingredients: Once ready to start baking, measure out another ½ cup of coconut oil and heat in the microwave until just melted (about 35 seconds). Set aside to cool to just about room temperature. Put eggs in a small bowl of warm (not hot) water. Allow to warm up for 5 minutes. Promptly drain the water from the bowl and set aside.
  4. Preheat oven and prepare pan: Preheat oven to 350°F (I use convection). Place 12 muffin liners in a standard-sized, 12-cup muffin pan and set aside. 
  5. Combine dry ingredients: In a large bowl, whisk together the dry ingredients: brown rice flour, tapioca flour, maple sugar, baking soda, baking powder, pumpkin pie spice, and salt. Set aside.
  6. Combine wet ingredients: In an extra-large bowl, whisk together all wet ingredients except for the zucchini: pumpkin puree, eggs, vanilla extract, apple cider vinegar, and coconut oil, adding the coconut oil last. 
  7. Combine dry and wet ingredients: Pour the dry ingredients into the wet ingredients and stir with a spoon until combined. Fold in shredded zucchini and stir until folded throughout the batter.
  8. Spoon batter into muffin liners: Using a dinner spoon, spoon dough into muffin liners until about full, evening out the batter in the cups once they all contain batter. If using it, sprinkle streusel topping on top of each muffin, making sure to use all of the streusel (pile on that streusel!)
  9. Bake, cool, and serve: Bake at 350°F on the center oven rack for 25-30 minutes or until an inserted toothpick comes out just about clean. Cool in the pan on a cooling rack for 10 minutes, then cool directly on the rack for an additional 10 minutes before serving. Cool completely before refrigerating.
  10. Storage: Store leftover low FODMAP pumpkin zucchini muffins in an airtight container in the refrigerator for up to 1 week.


  • Streusel topping: adds major deliciousness and a little bit of nice texture to the muffin, but also extra fat and calories. Nutritional information below includes the streusel topping. Monash University notes that fat can be an additional IBS trigger. The muffins are still amazingly delicious without the streusel topping and are a lot less crumbly. 
  • Pumpkin and zucchini: According to Monash University's Low FODMAP Diet App, pumpkin and zucchini both contain the FODMAP fructans. At the above quantities, combining pumpkin and zucchini amount to 75% of Monash's tolerable amount for fructans per serving. Sticking to one muffin per serving is low FODMAP; however, be mindful of what you may eat within the same 3-4 hours that may also contain fructans to avoid FODMAP stacking. Zucchini can be reduced to 1 cup to further mitigate the risk of FODMAP stacking. See post above for additional details.
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Category: Snacks
  • Method: Oven
  • Cuisine: American