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Home » Recipes » Breads

Healthy Carrot Apple Flax Muffins {GF, Low Cal}

Published: Aug 30, 2021 · Modified: Nov 2, 2023 by Megan

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Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients. These nutrient packed muffins are delicious and great for a portable snack! Low Calorie + Gluten Free

Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

Muffins always make Monday better, right? I like to call Monday "muffin Monday" because the on Monday you get to feast on all the muffins from the weekend's baking extravaganza. 

Click here to pin this recipe!

If you've been around here from the beginning of Skinny Fitalicious then you know I'm a lover of all things baking with carrots from raw carrot cake to Paleo carrot cake cookies and almond flour carrot cake. You could say I'm just a little obsessed with carrots! They're not only tasty, but just so easy to sneak into baked goods!

Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

Healthy Carrot Apple Flax Muffins

For these healthy carrot muffins, I did a spin on the almond flour morning glory muffins that are in my cookbook.

This version is made with gluten free flour and are lightly sweetened with cinnamon, applesauce and a bit of coconut sugar. They're also incredibly dense from the flaxseed which I love putting in baked good for healthy fat.

Here's a few more reason why I love these muffins!

  • Low Calorie - Calories matter for weight loss, but the numbers are not everything. You always want calories to be compromised of the nutrient dense ingredients which this recipe is. These muffins are 180 calories each!
  • Gluten Free - The ingredients in this recipe are gluten free.
  • Dairy Free - There is no dairy in this recipe.
  • Higher Protein - Each muffin has 3 grams of protein from the egg whites and flax meal. We always want to include protein in baked goods to offset the blood sugar response from the sugar.
  • High Fiber - Each muffin has 4 grams of fiber. Fiber is proven to aid in weight loss and hormone balance. I talk about the importance of fiber in this free weight loss class.
ingredients measured out for carrots and apples

Ingredients For Muffins with Carrots and Apples

Here's what you need to make gluten free carrot apple muffins. You will also need a muffin pan this is the one I use, avocado oil spray and large mixing bowl.

  • Carrots
  • Apples
  • Egg Whites
  • Applesauce, unsweetened
  • Extra Virgin Olive Oil
  • Gluten Free 1:1 Baking Flour
  • Flax Meal
  • Cinnamon
  • Baking Powder
  • Coconut Sugar
step by step illustration for apple carrot muffins

How To Bake Low Calorie Muffins with Carrots and Apples

These Healthy Carrot Apple Flax Muffins are super simple to make and kids will love helping you bake them too. Here's how you make them!

Step one is preheating the oven to 350 F and preparing a muffin tin. You can use muffin liners or spray the muffin cavities with avocado oil spray or olive oil spray.

Step two is mixing the blending the extra virgin olive oil, applesauce, egg whites and cinnamon using a standing mixer or hand mixer. You will blend until the egg whites become frothy and have bubbles.

Next add the coconut sugar, flax meal and baking powder while you continue to mix. Then fold in the flour to the mixture slowly while continuing to mix the ingredients on a low speed.

Last fold the apples and carrots into the batter and spoon the batter into the muffin cavities about 3/4 of the way full. Bake in the oven 25 to 30 minutes until a toothpick can be removed clean from the center. Cool in the pan 10 minutes before removing from the baking pan.

Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

How To Store Your Healthy Muffins

These muffins should be stored in the refrigerator or in the freezer in a container, in a storage bag or individually wrapped in plastic wrap. You can store them in the refrigerator up to 7 days or in the freezer up to 60 days. If you freezer the muffins, thaw them by removing from the freezer and placing in the refrigerator the night before you plan to eat them.

Substitutions For This Carrot Apple Flax Muffin Recipe

Here are the substitutions I recommend for this recipe. As always, substitutions you make will change the nutrition data you see in the recipe card below.

  • Apples - You can substitute shredded zucchini for the apples. If you do this, you will lose the sweetness that the apples add to the muffins. I recommend you 1 or 2 tablespoons of maple syrup to keep them tasting good!
  • Carrots - You could omit these if they don't work for you.
  • Extra Virgin Olive Oil - Olive oil can be baked with at temperatures 350 F and below. You can also use coconut oil or avocado oil as substitutes.
  • Applesauce - I have not tried substituting the applesauce in this recipe, but the batter does need this liquid to keep the muffins moist. You could consider using bananas or avocado to replace the applesauce, however, I have not tested this.
  • Egg Whites - You can substitute 1 whole egg for the 2 egg whites. If you do that, you will decrease the protein slightly as 2 egg whites have more protein than 1 whole egg.
  • Gluten Free Flour - I have not tested this recipe with other flours and I never bake with white or whole wheat flours. The only flour that can generally be swapped one-for-one with gluten free baking flour is oat flour. Always make sure you measure flours properly for baking too!
  • Flax Meal - The flax meal is critical to the recipe as it binds the batter and there is no replacement for this.
  • Coconut Sugar - Any sugar could be substituted for the coconut sugar. I prefer coconut sugar as it is slightly lower on the glycemic index than other sugar. Monkfruit would also work and will reduce the sugar content more if that is a concern for you. As a note, maple syrup and honey would not work.
Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

Click here to pin this recipe!

Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

Healthy Carrot Apple Flax Muffins

Megan Olson
Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients. These nutrient packed muffins are delicious and great for a portable snack! Low Calorie + Gluten Free
5 from 3 votes
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 30 minutes mins
Resting Time 5 minutes mins
Total Time 45 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 10 muffins
Calories 180 kcal

Ingredients
 
 

  • 1 cup carrots peeled (~2 medium carrots)
  • 2 apples peeled and cored
  • 2 egg whites
  • 1/2 cup unsweetened applesauce
  • 1/4 cup extra virgin olive oil
  • 1 1/2 cups Gluten Free 1 to 1 baking flour
  • 1/4 cup flax meal
  • 1 teaspoon cinnamon
  • 1 1/2 teaspoon baking powder
  • 1/3 cup coconut sugar

Instructions
 

  • Preheat oven 350 F. Line a muffin tin with muffin liners or spray with avocado oil spray or olive oil spray.
  • In a food processor, add the carrots and apples. Pulse a few times until shredded. Set aside.
  • In a standing mixer or using a hand mixer, add egg whites, olive oil, applesauce and cinnamon. Mix until eggs become frothy.
  • Add sugar, baking powder and flax and mix to combine. Then slowly add flour to the mixture while mixing on low.
  • Fold in the apples and shredded carrots into the batter.
  • Spoon batter into muffin cavities 3/4 full. Bake at 350 F 25 to 30 minutes until a toothpick can be removed clean. Remove from the oven and cool muffins in the pan 10 minutes before removing from the baking pan.
  • Store in the refrigerator in a sealed container up to 7 days or in the freezer up to 60 days.

Video

Notes

  • My Amazon shop has more products similar to those used for this recipe and that I recommend to my weight loss clients.
  • If you enjoy this recipe, check out my cookbook for more delicious and low calorie recipes.
  • Almond flour version of this recipe is in my cookbook.

Nutrition

Serving: 1muffinCalories: 180kcalCarbohydrates: 27gProtein: 3gFat: 8gSaturated Fat: 1gPolyunsaturated Fat: 2gMonounsaturated Fat: 4gSodium: 32mgPotassium: 193mgFiber: 4gSugar: 10gVitamin A: 2162IUVitamin C: 3mgCalcium: 58mgIron: 1mg
Tried this Recipe? Let me know!Let us know how it was!
Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.
Healthy Carrot Apple Flax Muffins are made low calorie, gluten free and dairy free with nutrient dense ingredients.

About Megan

Megan is a certified nutrition practitioner, author, freelance food photographer and fitness instructor living in Phoenix, Arizona. On her blog, Skinny Fitalicious she shares EASY, gluten free recipes for weight loss. Follow Megan on Facebook, Twitter, Pinterest and Instagram for the latest updates.

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    5 from 3 votes

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  1. lauren says

    November 01, 2023 at 12:37 pm

    Is it 350 or 375? It says both 🙂

    Reply
    • Megan says

      November 02, 2023 at 9:06 am

      It should be 350 F. Thanks for the catch!

      Reply
  2. Don Spatola says

    March 28, 2022 at 12:47 pm

    I bake your Perfect Paleo Bread recipe from Paleohacks often but didn't find that recipe here. I see you add Flax meal to many of your recipes. My question concerns the the stability of flax oil in flax meal at high temperatures. We are all aware of how quickly flax oil breaks down (oxidizes). Doesn't high temperatures speed up that process? Thank you.

    Reply
    • Megan says

      March 28, 2022 at 4:43 pm

      Flax oil and flax meal are not the same. Flax meal does not turn into oil during cooking. Flax oil should never be used in baking. Only as a finisher on cooked meal or as a dressing. Flax meal is, however, safe for baking. Paleo Hacks recipes are their recipes which is why they are on their website only - not here.

      Reply
  3. Annette says

    April 25, 2017 at 5:39 pm

    I just made these using almond flour. Very tasty but after 30 minutes (toothpick test appeared clean) they seem too moist in the center. Back in the oven for 10 more minutes......better.

    Reply
  4. Sherry says

    September 20, 2016 at 10:07 am

    what is GF 1 to 1 baking flour?

    Reply
    • Megan says

      September 20, 2016 at 11:13 am

      GF 1 to 1 baking flour

      Reply
  5. Miss Polkadot says

    March 29, 2016 at 11:37 am

    Flax fiends unite! I like to eat bowls of shredded carrots with a little coconut milk [not the canned one] and a sprinkle of flax. So good!
    These muffins look delightful and pack in so much goodness.

    Reply
    • Megan says

      March 29, 2016 at 4:45 pm

      Oh yum! It's Oatless flax oatmeal! I need to try.

      Reply
  6. Sam @ PancakeWarriors says

    March 28, 2016 at 6:55 pm

    Yummo I love how nourishing these are!! perfect for all those leftover carrots!!

    Reply
    • Megan says

      March 29, 2016 at 9:12 am

      Thanks girl!

      Reply
  7. Sarah @ Making Thyme for Health says

    March 28, 2016 at 5:45 pm

    These muffins look like the perfect healthy Easter treat! Carrot and apple make such a good combo.

    And I agree that Easter should be in April. I can never keep up with creating recipes in time for the holidays when there's more than one per month!

    Reply
    • Megan says

      March 28, 2016 at 5:49 pm

      Thank goodness we can eat muffins anytime!

      Reply
  8. rachel @ athleticavocado says

    March 28, 2016 at 9:48 am

    I love the carrot theme on your recipes lately! I'm always stoked up with baby carrots so this is perfect 🙂

    Reply
    • Megan says

      March 28, 2016 at 5:32 pm

      Thanks! Unfortunately, this is the last one for awhile. Tomorrow we have smoothies.

      Reply
      • Helen says

        August 27, 2022 at 7:25 pm

        What can I use in place of applesauce.

        Reply
        • Megan says

          August 29, 2022 at 8:28 am

          Maple syrup or honey.

          Reply
  9. Laura @ Sprint 2 the Table says

    March 28, 2016 at 9:14 am

    I used to make my apple carrot muffins alllll the time. I even made a protein version. Shockingly, I haven't made a muffin in months. Time to rectify that. Love the flax idea!!!

    Reply
    • Megan says

      March 28, 2016 at 5:31 pm

      An injury seems like the perfect time to start baking! P.S. I put flax or hemp in everything. Omega-3's!

      Reply
  10. Emily says

    March 28, 2016 at 7:20 am

    Mmm... yummy! I love all the flavors you combined here.

    Reply
    • Megan says

      March 28, 2016 at 5:29 pm

      Thank you Emily!

      Reply
  11. Lauren says

    March 28, 2016 at 7:19 am

    Oh love the combo of apple and carrot....yum!!!

    Reply
    • Megan says

      March 28, 2016 at 5:29 pm

      Thank Lauren!

      Reply
  12. Deborah @ Confessions of a mother runner says

    March 28, 2016 at 5:22 am

    Love the apple sauce in here and I love carrot muffins. Thanks for linking up!

    Reply
    • Megan says

      March 28, 2016 at 5:29 pm

      Applesauce is one of my favorite ways to cut down on sugar.

      Reply
  13. lindsay Cotter says

    March 28, 2016 at 4:39 am

    yay! can comment! and yay... I LOVE this combo! the addition of olive oil is lovely in baking.

    Reply
    • Megan says

      March 28, 2016 at 5:28 pm

      YAY for commenting again! I have chrome & safari and chrome is always giving me problems.

      Reply
  14. michele @ paleorunningmomma says

    March 28, 2016 at 3:52 am

    Love the carrot apple combo 🙂 Also I've never baked with olive oil and I'm intrigued!

    Reply
    • Megan says

      March 28, 2016 at 5:27 pm

      You can bake with it just like coconut oil. You just need to be careful not to go above it's smoke point.

      Reply
  15. Susie @ SuzLyfe says

    March 28, 2016 at 3:32 am

    Love the flavors of these! Carrot and apple are perfection together, as long as you don't let them get too sweet, but a muffin usually helps keep that from happening.

    Reply
    • Megan says

      March 28, 2016 at 5:26 pm

      You will like these then, they're not very sweet at all. Watching my sugar!

      Reply
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Megan is a nutritionist, author of the Low Calorie Cookbook and podcast host of the Dish On Ditching Diets. Megan helps women over 35 stop dieting, heal their relationship with food and lose weight sustainably. Megan lost 80 pounds herself. Here you get healthy, lower calorie recipes!

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