Spiced Carrot Muffins

What if I asked you to make me breakfast? It couldn’t be that hard, right? Here are the guidelines: it must be grain-free, egg-free, dairy-free, corn-free, fruit-free, soy-free, no refined sugars, low sulfur.  Have you thought of anything yet? I am waiting…

When I first started following a modified version of the SIBO specific food guide, I completely gave up the idea of breakfast and began to see all of my meals as equal.  At first, I felt empowered that I did not have to eat a sugary treat for breakfast, but eventually I found myself dreading eating breakfast or constantly being late because it took too much time to prepare my dinner-like meals.

I decided that I had to find a happy medium.  I created these Spiced Carrot Muffins as a convenient option for a SIBO-friendly breakfast.  They are very minimally sweetened (only 1 teaspoon of maple syrup or honey per muffin) and that makes me feel good about serving them for the most important meal of the day.  To make a complete meal, I like to serve my muffin warm with ghee or butter alongside a glass of almond milk and a turkey sausage.  To turn this recipe into a dessert, I recommend serving with homemade frosting or adding chocolate chips.

Spiced Carrot Muffins

  • Servings: 9
  • Difficulty: easy
  • Print

Low FODMAP, paleo, SCD, SIBO specific food guide, soy-free, dairy-free, grain-free, gluten-free, egg-free, low thiol

carrot muffins

Kitchen Supplies:

  • muffin tin
  • 9 large baking cups
  • medium-sized mixing bowl & small mixing bowl
  • measuring spoons & cups
  • spoon for stirring


  • 1.5 cups almond flour
  • 2 teaspoons baking powder (for paleo: 1/2 teaspoon baking soda + 1 Tablespoon lemon juice or vinegar)
  • 1.5 teaspoons ground cinnamon
  • 1/2 teaspoon sea salt
  • 1/2 teaspoon ground nutmeg
  • 1/4 teaspoon ground cloves
  • 1 cup carrots, grated
  • 3 Tablespoons coconut oil, melted
  • 3 Tablepsoons maple syrup or melted honey
  • 1.5 flax “eggs” (1.5 Tablespoons of ground flax meal + 4.5 Tablespoons water)
  • 1.5 teaspoons pure vanilla extract


  1. Preheat oven to 350 degrees.
  2. In a small bowl, combine flax seed and water.  Set aside.
  3. In the large mixing bowl, add dry ingredients: almond flour, baking powder, cinnamon, sea salt, nutmeg, and cloves.
  4. Add carrot, melted coconut oil, sweetener, and vanilla extract to the flax egg mixture. Stir to combine.
  5. Fold wet ingredients into dry ingredients until well combined.
  6. Line muffin tin with baking cups.  Transfer equal amounts of batter into each of the 9 baking cups.
  7. Bake for 35-40 minutes or until edges brown slightly and a fork can be inserted and come out clean.
  8. Serve warm.  Consider topping with butter, ghee, and/or honey.

10 thoughts on “Spiced Carrot Muffins

  1. Hi, the carrot muffins look really delicious. I am just wondering about how low Fodmap they really are. I read that 1 cup almond flour consists of approx. 90 almonds and allowed are only 10 per sitting. This would mean at least 15 in one muffin. And how about the maple syrup? According to Dr. Siebecker’s List it is SCD illegal… Do you tolerate the muffins? Many thanks.


    • Hi Christine,

      You bring up a good point. I did not sit down and actually calculate out the amount of almonds in each muffin, so they may not be strictly low FODMAP. I would say that if you are concerned that they are not quite low FODMAP enough, go ahead and either make more muffins out of the mix so they are smaller or try using a different flour such as macadamia. I tolerated them just fine, but it was not during the beginning of my healing, so it could certainly be different for you based on where you are on your journey. In terms of the maple syrup, you could always substitute honey. I cannot quite remember why I did not use honey (perhaps I was out). SCD was originally intended for individuals with inflammatory bowel conditions such as crohn’s and ulcerative colitis so I found that I was actually able to tolerate a certain amount of grains as my healing progressed and they significantly improved my fatigue, thyroid health, and took me out of amenorrhea. Point being that I think it is important to not just follow a list but try different foods and see how your body responds.


    • Hi Julia,

      I have an intolerance to high thiol foods (including eggs), which is why I created this recipe with flax. I think that it would actually probably taste better with egg. According to Dr. Siebecker’s food guide, less than 1 tablespoon of flax is considered “Moderate FODMAP”. It could bother some people, but personally, I do quite well with these muffins & with flax meal.


    • Let me know how they turn out! The recipe is not very sweet- my dad thinks they are perfect, but he always complains about things being too sweet so others may find these muffins to be not sweet enough.


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