Enjoy the best of both summer and fall with these Low FODMAP Pumpkin Zucchini Muffins! Made with a combination of gluten-free brown rice flour and tapioca flour and low FODMAP quantities of pumpkin and zucchini, these moist 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. These low FODMAP muffins are also kid-friendly, gluten-free, dairy-free, and refined sugar-free.
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Why Low FODMAP Pumpkin Muffins with Zucchini?
I don't garden other than a small patio herb garden when I feel like it (which I usually don't). However, all of our surrounding neighbors garden and give us some of their garden spoils from time to time. While I appreciate these gifts, as I plan my meals well in advance of cooking, I sometimes find it challenging to find a way to use them before they go bad. You may find this challenging, too.
This low FODMAP pumpkin zucchini muffin recipe has made using up garden zucchini - however you obtain it - a little bit easier. They're quick to make and are ideal for a late summer / early - late fall low FODMAP snack. It's also a great gateway recipe into pumpkin spice season. If you're not fully ready to give up summer yet but you're somewhat eager to give a nod to fall recipes - this low FODMAP pumpkin zucchini muffin recipe is for you.
If you're looking for a low FODMAP pumpkin recipe that fully embraces fall, try my Low FODMAP Pumpkin Bread recipe.

A Note on FODMAPs
According to Monash University's Low FODMAP Diet App, pumpkin and zucchini both contain the FODMAP fructans. Tolerable serving sizes are listed as ⅓ cup or 75 grams for pumpkin and ⅓ cup or 65 grams for zucchini. This recipe calls for 1 cup of pumpkin and 2 cups of zucchini across 12 servings. At these quantities, combining pumpkin and zucchini amount to 75% of Monash's tolerable amount for fructans per serving. Sticking to one pumpkin zucchini muffin per serving is low FODMAP.
However, something to keep in mind as this is a snack recipe - eating something else within 3-4 hours of this pumpkin zucchini muffin that also contains fructans may put one at risk for FODMAP stacking. While there is a bit of wiggle room, just something to keep in mind. If you are concerned about the chance of FODMAP stacking, you can always reduce the quantity of zucchini to 1 cup. It kind of disappears into the muffin at that amount but will lessen the risk of FODMAP stacking and still sneak in some green veggies.
Necessary Equipment
The equipment I use to make these low FODMAP Pumpkin Zucchini Muffins includes:
- Gas or electric oven (I use an electric convection oven)
- Standard sized 12-cup muffin pan
- 12 muffin liners
- Small, large and extra large bowls
- Fork or pastry knife (for optional streusel topping)
- Whisk
- Stirring spoon
- Dinner spoon
- Toothpick
- Wire cooling rack

Low FODMAP Pumpkin Zucchini Muffins: Ingredients & Success Tips
Streusel Topping (Optional)
If you want to add some extra mouthwatering flavor (although also extra fat and calories) to your low FODMAP pumpkin zucchini muffins, I have added instructions for how to make a streusel topping. The streusel makes them more of a dessert muffin, so if you're looking for a less sugar-y, less fattening, less crumbly low FODMAP muffin - skip the streusel topping. The muffins are still delicious without it. Additionally, Monash University states excess fat can be an additional IBS symptom trigger.
To make the low FODMAP streusel topping, I add brown rice flour, maple sugar, solid and pre-chilled coconut oil, pumpkin pie spice, and salt to a small bowl and mash the ingredients together with a fork or pastry knife until combined and crumbly. Then, I stick it in the refrigerator to chill until I'm ready to add it to the top of the muffins.
Prepare Coconut Oil & Eggs
To start making the low FODMAP pumpkin zucchini muffins, I measure out the coconut oil for the muffins (not the oil for the streusel - we want that oil to be solid) and heat it in the microwave until just melted. This takes about 35 seconds with my microwave. Then, I set it in a cool place to cool to just above room temperature. I typically put it in the refrigerator to cool off, but I have to be sure not to leave it in there too long or else it will re-solidify.
Then, I put my eggs in a small bowl of warm water for 5 minutes to bring them to room temperature. It's important that the water is warm, not hot, as we don't want the eggs to actually cook, we just want to warm them to room temperature. After 5 minutes, I promptly drain the water from the bowl and set the eggs aside.
While a bit of a pain, bringing your ingredients to room temperature will help promote even baking as well as keep your coconut oil from solidifying when added to the other ingredients.
Preheat Oven & Prepare Pan
After the streusel is prepared, I preheat my oven to 350°F, using the convection setting. If you don't have a convection oven, your muffins will probably take longer to bake. It's best to check them at (or a few minutes prior to) the listed baking time so that they don't overbake.
I also get my muffin pan ready, adding a paper liner to each cup.

Dry Ingredients
In a large bowl, I whisk together the following dry ingredients:
- Brown rice flour - can be purchased on Amazon and many mainstream grocery stores.
- Tapioca flour - can be purchased on Amazon or in some health food stores and mainstream grocery stores.
- Maple sugar - can be purchased on Amazon or in some health food stores.
- Baking soda
- Baking powder
- Pumpkin pie spice - I use my own homemade recipe, but you can also use a store-bought pumpkin pie spice, which are typically low FODMAP but may contain potentially harmful additives.
Wet Ingredients
In an extra large bowl, I whisk together the following wet ingredients:
- Canned pumpkin puree - When you buy it, ensure it's not pumpkin pie filling, which can also be purchased in a can.
- Large eggs, at room temperature
- Pure vanilla extract
- Apple cider vinegar
- Coconut oil, melted and just above room temperature
Then, I add the dry ingredients to the wet ingredients and stir with a spoon until combined.
Zucchini
I coarsely grate the zucchini and do not dry it off. Some zucchini bread/muffin recipes will tell you to dry it with paper towels, but unless your zucchini is sopping, dripping wet, I highly recommend not drying it off as we want that moisture to go into our muffin. This is one of the biggest advantages of using vegetables and fruits in baking - they add moisture. If you remove that moisture, you're removing this advantage.
Also, I do not finely grate the zucchini as this will cause it to completely disappear within the muffin. We want our zucchini to shine.
Once ready to go, I fold the zucchini into the muffin batter until thoroughly combined.

Spoon Batter into Muffin Liners
I use a dinner spoon to spoon the batter into the muffin liners until they're just about full. Then, I use the spoon to even them out as needed. It's okay if they're piled a bit over the top of the edge of the liner as long as they're mostly even.
I then top with the streusel, crumbling it with my fingers over the top, making sure to use all of it. It may seem like a lot when you put it on, but much of it will melt into the muffin when it's baking.
Bake, Cool, & Serve
I bake the muffins for 25-30 minutes at 350°F on the center oven rack. Once an inserted toothpick comes out clean, I remove them from the oven, cooling them first in the pan on top of a cooking rack for 10 minutes. Then, I remove them from the pan and cool them directly on top of the rack for another 10 minutes. I like to serve them warm, but they're still quite good cold or at room temp, too.
Storage
I store these low FODMAP pumpkin zucchini muffins in an air tight container in the refrigerator for up to 1 week, but they rarely last that long as my family enjoys them so much.


Low FODMAP Pumpkin Zucchini Muffins (Gluten-Free)
Ingredients
Low FODMAP Streusel Topping (Optional)*
- ½ cup brown rice flour
- ½ cup maple sugar
- ½ cup coconut oil, solid and chilled
- 2 teaspoons pumpkin pie spice, homemade or store-bought
- ¼ teaspoon salt
Dry Ingredients
- 1 cup brown rice flour
- ½ cup tapioca flour
- ½ cup maple sugar
- 2 teaspoons baking soda
- ½ teaspoon baking powder
- 1 ½ teaspoons pumpkin pie spice, homemade or store-bought
- ½ teaspoon salt
Wet Ingredients
- 1 cup canned pumpkin puree*
- 3 large eggs, room temperature
- 1 teaspoon pure vanilla extract
- 1 teaspoon apple cider vinegar
- ½ cup coconut oil, melted and just above room temperature
- 2 cups zucchini, coarsely grated (about 1 medium zucchini)*
Instructions
- {Optional} Prepare your streusel ingredients: About ½ hour prior to baking, stick ½ cup of solid coconut oil in the refrigerator to chill.
- {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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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!)
- 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.
- Storage: Store leftover low FODMAP pumpkin zucchini muffins in an airtight container in the refrigerator for up to 1 week.
Notes
- 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.
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