Low FODMAP Pumpkin Flaxseed Muffins (Gluten-Free)
If you’re looking for a delicious and gut-friendly treat this fall, these Low FODMAP Pumpkin Flaxseed Muffins are just what you need! Packed with the warm flavors of pumpkin and spices, these muffins are perfect for a cozy breakfast or a satisfying snack.

Adding flaxseed boosts their nutritional value and adds a nice nutty flavor. Best of all, they’re low FODMAP and gluten-free, making them a great option for those with digestive issues or anyone following a low FODMAP diet.
Making pumpkin muffins or pumpkin bread is a treat I look forward to in the fall months. I’m so glad I created this recipe to share with you. It tastes so good and is a great way to increase your fiber. Getting enough fiber in your diet can be challenging, especially while on the Low FODMAP diet. If you need more ideas on how to get more fiber, read my post on High Fiber Low FODMAP Foods!
Why You’ll Love This Recipe!
- Gluten-Free and Low FODMAP: These muffins are perfect for anyone following a gluten-free or low FODMAP diet. They allow you to enjoy a tasty treat without worrying about digestive discomfort.
- Nutrient-Packed with Flaxseed: Adding ground flaxseed boosts fiber and omega-3s, making these muffins both wholesome and satisfying.
- Rich Pumpkin Flavor: Packed with real pumpkin puree and warm spices, these muffins deliver the cozy flavors of fall in every bite.
- Freezer-Friendly: These muffins can be made ahead and frozen, making them a convenient snack or breakfast option for busy days.
Ingredients and Substitutions
- Avocado Oil Cooking Spray: Use cooking spray to lightly coat the muffin liners, preventing the muffins from sticking while keeping the recipe light and health-conscious.
- Eggs: Provide structure and moisture to the muffins, helping them rise and hold their shape.
- Light Brown Sugar: Adds sweetness with a hint of molasses flavor, complementing the warmth of the pumpkin and spices.
- Granulated Sugar: Balances the sweetness in the muffins, ensuring the right texture and flavor.
- Canned Pumpkin Purée: Pumpkin is the star, giving these muffins their delicious pumpkin flavor while adding moisture and nutrients like fiber and vitamin A.
- Coconut Oil or Avocado Oil: These healthy fats contribute to the muffins’ moisture and tenderness while keeping the recipe dairy-free.
- Vanilla Extract: Enhances the flavor of the muffins by adding a subtle, sweet, aromatic note.
- Gluten-Free Flour (1:1): This gluten-free blend directly substitutes for regular flour, ensuring the muffins are light and fluffy and suitable for those with gluten sensitivities.
- Ground Flaxseed: A nutritious addition that boosts the fiber and omega-3 content, adding a slight nuttiness to the muffins.
- Baking Powder: Helps the muffins rise and become light and airy during baking.
- Baking Soda: Works alongside the baking powder to create a perfect rise, giving the muffins a nice dome shape.
- Salt: Enhances all the flavors, balancing sweetness and bringing out the pumpkin and spice notes.
- Pumpkin Pie Spice: This blend of warm spices (like cinnamon, nutmeg, and cloves) amplifies the fall flavors.
- Semi-Sweet Chocolate Chips (optional): These add a rich, indulgent sweetness to the muffins, making them a bit more of a treat while perfectly complementing the pumpkin.

Step-by-Step Instructions
Step 1: Preheat your oven to 425°F. Line a 12-count muffin pan with liners, then lightly spray them with nonstick cooking spray. Set the pan aside.
Step 2: In a large mixing bowl, whisk together the eggs, brown sugar, granulated sugar, pumpkin puree, oil, and vanilla until well combined. Next, add the gluten-free flour, ground flaxseed, baking powder, baking soda, salt, and pumpkin pie spice to the wet mixture. Gently whisk until just combined, being careful not to overmix. If adding chocolate chips, fold them in the batter, setting aside a few to sprinkle on top of the muffins. The batter will be thick.


Step 3: Fill each muffin cup to the brim, allowing the batter to slightly overflow. Top the unbaked muffins with the reserved chocolate chips.

Step 4: Bake the muffins at 425°F for 5 minutes, then, without removing them from the oven, lower the temperature to 350°F. Continue baking for an additional 15-18 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Step 5: Once done, remove the muffins from the oven and let them cool in the pan for 5-10 minutes. Then, transfer them to a wire cooling rack to cool completely.

Step 6: Store the pumpkin muffins in an airtight container at room temperature for up to 5 days, or freeze them for up to 3 months.
Storage Instructions
For best results, store your pumpkin flax muffins using the following methods:
- Room Temperature: Store the muffins in an airtight container at room temperature for up to 5 days. This keeps them fresh and soft.
- Refrigeration: To extend the muffins’ shelf life, you can refrigerate them in an airtight container for up to 7 days. Be sure to let them come to room temperature or warm them slightly before enjoying them.
- Freezing: To freeze, allow the muffins to cool completely, then place them in a freezer-safe bag or container. They can be frozen for up to 3 months. When ready to eat, thaw at room temperature or microwave for a few seconds until warmed through.
Low FODMAP Information
The ingredients in these Pumpkin Muffins are low FODMAP. I checked each serving using the Monash University Low FODMAP app to ensure they were within the recommended serving sizes. So, if you are following a low FODMAP diet, you can enjoy one muffin per meal.
- Ground flaxseeds are a great way to add fiber to your diet and are low in FODMAP. You can consume up to 1 tablespoon per meal.
- Canned pumpkin is low in FODMAPs, up to ⅓ cup per meal.
- Gluten-free flour is also low in FODMAPs, up to ⅔ cup per meal.
More Low FODMAP Breakfast Recipes

Pumpkin Flaxseed Muffins
Ingredients
- cooking spray avocado or olive oil
- 2 large eggs
- ¾ cup light brown sugar lightly packed
- ¼ cup granulated sugar
- 1 cup canned pumpkin puree
- ½ cup coconut oil or avocado oil
- 1 teaspoon vanilla extract
- 1¾ cups 1:1 gluten-free flour
- ½ cup ground flaxseed
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 2 teaspoons pumpkin pie spice
- 1 cup semisweet chocolate chips optional
Instructions
- Preheat your oven to 425°F. Line a 12-count muffin pan with liners, then lightly spray them with nonstick cooking spray. Set the pan aside.
- In a large mixing bowl, whisk together the eggs, brown sugar, granulated sugar, pumpkin puree, oil, and vanilla until well combined. Next, add the gluten-free flour, ground flaxseed, baking powder, baking soda, salt, and pumpkin pie spice to the wet mixture. Gently whisk until just combined, being careful not to overmix. If adding chocolate chips, fold them in the batter, setting aside a few to sprinkle on top of the muffins. The batter will be thick.
- Fill each muffin cup to the brim, allowing the batter to slightly overflow. Top the unbaked muffins with the reserved chocolate chips.
- Bake the muffins at 425°F for 5 minutes, then, without removing them from the oven, lower the temperature to 350°F. Continue baking for an additional 15-18 minutes or until a toothpick inserted into the center of a muffin comes out clean.
- Once done, take the muffins out of the oven and let them cool in the pan for 5-10 minutes. Then, transfer them to a wire cooling rack to cool completely.
- Store the muffins in an airtight container at room temperature for up to 5 days, or freeze them for up to 3 months.
Notes
Storage Instructions
For best results, store your pumpkin flax muffins using the following methods:- Room Temperature: Store the muffins in an airtight container at room temperature for up to 5 days. This keeps them fresh and soft.
- Refrigeration: To extend the muffins’ shelf life, you can refrigerate them in an airtight container for up to 7 days. Be sure to let them come to room temperature or warm them slightly before enjoying them.
- Freezing: To freeze, allow the muffins to cool completely, then place them in a freezer-safe bag or container. They can be frozen for up to 3 months. When ready to eat, thaw at room temperature or microwave for a few seconds until warmed through.
