Easy Cinnamon Bun Flaxseed Muffins are a low-carb nutritional powerhouse! This healthy baking idea is gluten-free, low in sugar, and good for breakfast or snack time!

This is a great keto recipe! Other healthy breakfast ideas include Banana Almond Butter Muffins and Easy Oatmeal Bars. 

Healthy Alert! These Cinnamon Bun Flaxseed Breakfast Muffins pack a hearty amount of nutritional goodness in every bite! Plus, they’re low in sugar, so they don’t taste overly sweet, but they’re totally satisfying.

They’re also gluten-free! You can even make them Keto if you like!

Are Flax Muffins Good for You?

If you need a little fiber in your diet, and let’s be honest, who doesn’t! Yes, Flax Muffins are good for you. Fiber has so many benefits besides keeping you regular, like:

  1. Fiber slows the rate that sugar is absorbed into the bloodstream, which keeps your blood sugar levels from rising too fast. Awesome!
  2. It lowers cholesterol levels. Soluble fiber found in beans, oats, flaxseed, and oat bran may lower total blood cholesterol levels by lowering low-density lipoprotein or “bad” cholesterol levels. Good news!
  3. Aids in achieving a healthy weight. No empty calories here! High-fiber foods tend to be a bit more filling than low-fiber processed foods, so you’re likely to eat less and stay satisfied longer, which helps with weight loss.

So yes, lots of benefits, but kids and grown-ups like these low-carb muffins, so let’s get to the easy recipe!

Flaxseed Breakfast Muffins on a cooling rack.

Ingredient Notes and Substitutions

If your dietary requirements need it, this low carb muffin does not contain all-purpose flour, almond flour, or coconut flour but does contain healthy fats in coconut oil. 

  • Ground flaxseeds – these are also called milled flaxseed or flax meal. They add a pleasant, earthy flavor and satisfying texture to these homemade muffins. You can usually find them in the baking aisle in the grocery store, and Costco often carries them.
  • Honey or brown sugar – either works well in the recipe to create a slightly sweet muffin. You can also substitute maple syrup. 
  • Ground cinnamon – gives the muffins a sweet, woody flavor and makes them reminiscent of sweet cinnamon buns. You can also add a small amount of nutmeg if you’d like.
  • Baking powder and baking soda – are used as leavening agents. Just make sure they’re fresh. You’ll omit the baking soda if using brown sugar as your sweetener.
  • Eggs – acts as the binder in the recipe. 
  • Pure Vanilla extract – enhances the flavors of other ingredients like sugar and flaxseeds. 
  • Coconut oil – works as a butter substitute and makes this recipe vegan. 

How to make Flax Muffins

This easy breakfast makes 12 flax muffins, so if you want, you can double the recipe and freeze some for later!

It’s always smart to cook/bake once and eat twice!

This Gluten-Free Peanut Butter Cookie recipe is proof of that! It’s so nice to have a few waiting in the freezer when a craving strikes!

Step 1

First, you need to preheat your oven to 350 degrees F. (180 c). Then, you can either get out your silicone muffin pan, as we like to do or line a muffin pan with paper liners.

Step 2

In a large bowl, you need to combine your dry ingredients. Whisk your flaxseeds with cinnamon, baking powder, baking soda, and salt.

Flaxseeds, cinnamon, baking soda and baking powder in a bowl.

Step 3

Next, it’s time to mix your wet ingredients. Place eggs, water, melted coconut oil, vanilla, and honey in a blender. Blend on high speed for about 30 seconds either in a blender or food processor.

PRO TIP: If your coconut oil is solid, melt it slightly in the microwave. 

You should whip your mixture until foamy.

blender with eggs, oil, vanilla in it.

Step 4

Now, mix your wet ingredients into your dry ingredients with a spatula just until combined.

Wet and dry ingredients blended together to make flax muffins.

The batter will be a little fluffy.

Step 5

Place the batter in your muffin pan, filling each cup almost to the top—about 90 percent. We like to use a cookie scoop, which makes it way easy!

low carb muffins in a silicone muffin pan.

Step 6

Bake for approximately 13-15 minutes. You can check by inserting a toothpick in the middle, and if it comes out clean, they’re done.

Finally, take your muffins out of the pan and let them cool on a cooling rack.

Now, it’s time to bite into your delicious flax muffin recipe!

Recipe Tips and Tricks

  • If you use erythritol or stevia, these work as Keto Flaxseed Muffins or Keto snacks!
  • These Healthy Muffins freeze well, so they’re a great make-ahead breakfast or snack.
  • The decorative fruit topping is optional but does give them a little personality!

How to Make Keto Flaxseed Muffins

As mentioned, you can totally make this a low carb option and Keto-friendly by using erythritol or stevia instead of sugar or honey.

  • Add 1/3 cup erythritol to the dry ingredients or 3/4 teaspoon liquid stevia to the wet ingredients. Then you’ll have the perfect keto snack when done

How to Freeze 

It’s easy to freeze these flax muffins and get them out when ready to eat. Place baked muffins in a freezer bag or airtight container, and keep them in the freezer for up to 3 months.

Either microwave for a few seconds to defrost or place in the refrigerator until ready to eat.

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flaxseed muffin with a raspberry on top.
5 from 7 reviews

Cinnamon Bun Flaxseed Muffins Recipe

Servings: 12
Prep Time: 10 minutes
Cook Time: 15 minutes
cooling time: 15 minutes
Total Time: 25 minutes
Easy Cinnamon Bun Flaxseed Muffins are a low carb nutritional powerhouse! This healthy baking idea is gluten-free, low in sugar, and good for breakfast or snack time!
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Ingredients
 

  • 2 cups ground flaxseeds
  • ⅓ cup honey, or ½ cup brown sugar
  • 2 tablespoons ground cinnamon
  • 1 tablespoon baking powder
  • ¼ teaspoon baking soda, omit if using brown sugar
  • ½ teaspoon sea salt
  • 5 large eggs
  • ⅓ cup water, room temperature *
  • ⅓ cup coconut oil, melted
  • 2 teaspoons vanilla extract

Equipment

  • muffin tin
  • mixing bowl
  • whisk
  • Blender
  • Spatula or cooking spoon

Instructions
 

  • Preheat oven to 350 degrees F (180 C).  Line the muffin pan with paper liners or get out the silicone baking pan if using. 
  • In a large bowl, whisk together flaxseeds, cinnamon, baking powder, baking soda, and salt.  
  • Place eggs, water, oil, vanilla, and honey in a blender.  Blend on high speed for about 30 seconds. The mixture should be whipped until slightly foamy. 
  • Now, mix wet ingredients into your dry ingredients with a spatula just until incorporated. The batter will be a little fluffy. 
  • Place the batter in your muffin pan, filling each cup almost to the top. About 90 percent. Bake for approximately 13-15 minutes. You can check by inserting a toothpick in the middle, and if it comes out clean, they're done. 
  • Wait 2 minutes, then take muffins out of muffin pan and cool for 15 minutes on a cooling rack. Enjoy! 

Notes

You can substitute the sugar in this recipe for a sugar substitute like:
1/3 cup erythritol or 3/4 teaspoon liquid stevia. 
*If using brown sugar, use 1/2 cup water.
Keep in the refrigerator for about 5 days or freeze for up to 3 months. 
Nutritional information is approximate and was calculated using a recipe nutrition label generator and will vary based on cooking methods and brands of ingredients used.
Calories: 285kcal, Carbohydrates: 17g, Protein: 7g, Fat: 22g, Saturated Fat: 9g, Cholesterol: 77mg, Sodium: 159mg, Potassium: 357mg, Fiber: 8g, Sugar: 8g, Vitamin A: 115IU, Vitamin C: 0.2mg, Calcium: 136mg, Iron: 2.1mg
Did you make this recipe?Mention @suburbansimplicity on Instagram or use the hashtag #suburbansimplicity!

This recipe was published in 2018 and was updated and reviewed in 2024.