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low fodmap flax muffins

Low FODMAP Flax Muffins for IBS and Constipation

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[Updated May 2025]

For those of you with IBS-C (constipation predominant) or IBS-M (mixed constipation alternating with diarrhea), this low FODMAP flax muffin with blueberries is an easy and delicious way to promote better bowel regularity and stick to the low FODMAP diet at the same time.

Low FODMAP Ingredients & Alternatives

Ingredients for low fodmap flax muffins.

Ground Flax. Ground flax is low FODMAP at 1 Tbsp and high FODMAP at 2 Tbsp, according to the Monash FODMAP app, so I crafted this recipe to contain 1 Tbsp ground flax per muffin to keep it low FODMAP AND still benefit constipated bowels.

One to two tablespoons (1-2 Tbsp) of ground flax daily can improve constipation, making these muffins ideal for people with constipation-predominant IBS. I categorize ground flax as a “laxation food” since it has unique constipation-fighting abilities similar to oats, prunes and kiwis.

In addition to containing 2 grams of fibre per tablespoon and promoting bowel regularity, ground flax slows digestion and is rich in omega-3 fats that help minimize inflammation.

Ground flax isn’t a terribly tasty or exciting ingredient to add to foods, and 1-2 Tbsp is a lot to add to a yogurt parfait or oatmeal. Therefore, this muffin is an attempt to help people with constipation get some variety in the way that they consume flax.

Almond Flour. Almond flour helps to give this muffin nutty flavour notes, which I love, and is low FODMAP at 1/3 cup. Since we’re using 1/2 cup between 12 muffins, the muffin includes a low FODMAP serving size of almond flour.

Because almond flour can make baked foods crumble and fall apart more easily, I’ve used 3 eggs in this recipe to help bind the flours in this muffin.

Gluten-Free Flour. Gluten-free flour is low in fructans, which is why we use it in the low FODMAP diet.

Bob’s Red Mill Gluten-Free 1-to-1 Baking Flour is a gluten-free “all-purpose” flour, and does a decent job of replacing all-purpose wheat flour in baked goods. In fact, it’s my go-to gluten-free flour for baking.

Table with a variety of healthy foods like fruits, vegetables, nuts, oil, milk, eggs, fish.
Read all about the low FODMAP diet here.

Apple. Apple is considered a “no-no” food on the low FODMAP diet because it’s very high in two FODMAP groups: sorbitol and fructose. Sorbitol and fructose draw extra water into the intestine which triggers gut motility. For people with constipation, fruits high in sorbitol and fructose can help keep the bowels moving, but for people with diarrhea, sorbitol and fructose can exacerbate loose BMs.

Apple is low FODMAP at 23 grams, and since this flax muffin recipe calls for 50 grams in 12 muffins, each muffin has a very low FODMAP serving size of apple.

With moisture-absorbing ground flax, flour and almond meal, this muffin could easily become dry and crumbly. The grated apple adds flavour and moisture, and does a wonderful job of preventing the muffins from drying out.

Blueberries. Blueberries are low FODMAP in serving sizes up to 1 cup, making them a very popular fruit among people on the low FODMAP diet.

When making muffins and pancakes, I love to use frozen wild blueberries because they’re sweet, packed with fruity flavour, and small so you don’t end up with a big wet glob in the middle of the muffin. Oh, and the potent antioxidant content in blueberries makes them a fantastic inflammation-fighting food.

Lactose-Free Milk. Lactose-free milk is a nutrient-dense food containing protein, calcium, vitamin D, vitamin A and vitamin B12. If you don’t drink cow’s milk, almond milk and oat milk (up to 1/2 cup per serving) are low FODMAP alternatives you could use in this recipe.

When buying a milk alternative like almond milk, always check the Nutrition Facts Table to make sure that it is fortified with calcium and vitamin D.

A dozen baked low fodmap flax muffins with blueberries for fighting constipation

What to Serve with Low FODMAP Flax Muffins

These muffins are high fibre and nutritious (yes still delicious!) so they can certainly be eaten as part of a balanced breakfast or a hearty low FODMAP snack. Some ideas:

  • Pair with 1 Tbsp almond butter.
  • For an easy grab-and-go breakfast, enjoy this muffin with a firm banana and a couple babybel cheese.
  • For a mid-morning snack, nosh the muffin with a lactose-free latte.
  • Bring one along for a weekend hike.

Tips for Success

Don’t be tempted to replace the almond flour with more gluten-free flour because the almond flour really gives these muffins a subtle nutty flavour that’s oh-so-nice and helps to keep the muffin moist as well on account of its high fat content.

Single flax muffin with blueberries

Low FODMAP Flax Muffin with Blueberries

These low FODMAP high fibre flax muffins are constipation-fighting ninjas with subtle nutty sweetness and a moist crumb.
Prep Time 10 minutes
Cook Time 20 minutes
Course Breakfast, Snack
Cuisine American
Servings 12
Calories 285 kcal

Ingredients
  

  • 1/2 cup almond flour
  • 3/4 cup ground flaxseed
  • 1 1/4 cup gluten-free flour, I used Bob's Red Mill 1-to-1 gluten free baking flour
  • 1 tsp baking powder
  • 1/2 tsp salt
  • 2 tsp cinnamon
  • 1/2 tsp nutmeg
  • 3 eggs, large
  • 1/2 cup lactose-free milk
  • 3/4 cup brown sugar
  • 1/2 cup vegetable oil
  • 50 grams grated apple
  • 3/4 cup frozen wild blueberries

Instructions
 

  • Pre-heat oven to 350F / 180C.  Line muffin tin with muffin liners, or spray muffin pan with nonstick cooking spray.
  • In a large bowl, mix all the dry ingredients together (first 7 ingredients).
  • In a medium bowl, whisk eggs, then milk and brown sugar, followed by oil and grated apple.
  • Pour wet ingredients into the dry ingredients and gently stir with a wooden spoon until just combined.
  • Gently fold in frozen blueberries.
  • Fill muffin paper liners about 3/4 full.
  • Bake for 18 minutes until tops are cracked and slightly golden.
  • Cool on a wire rack.

Notes

Store in an airtight container at room temperature, or in the freezer.  These muffins are delicious slightly warmed in the microwave.

Nutrition

Serving: 1gCalories: 285kcalCarbohydrates: 29gProtein: 6gFat: 17gSaturated Fat: 2gPolyunsaturated Fat: 8gMonounsaturated Fat: 3gTrans Fat: 0.1gCholesterol: 42mgSodium: 159mgPotassium: 143mgFiber: 5gSugar: 16gVitamin A: 84IUVitamin C: 1mgCalcium: 98mgIron: 2mg
Keyword flax muffin, flax muffin recipe, low FODMAP muffin
Tried this recipe?Let us know how it was!
Flat lay of high fibre food like chia seeds, lentils, whole grain pasta and bread, kiwi, broccoli, oranges, etc.

Thanks for stopping by to check out my recipe. Happy noshing!

xoAndrea, RD

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