I love this moist savory gluten-free carrot muffins recipe with apples for so many reasons!
- They're easy to make: all the ingredients go in one bowl
- They're pretty healthy: packed with proteins from flaxseed meal, eggs and optional ad-ins, as well as reduced amount of sugar (check out this post from A Sweet Pea Chef about the benefits of flaxseed meal)
- They're customizable: you can add pecans, walnuts, raisins, anything you desire to really make them your own
- They stay moist: gluten-free baked goods tend to be dry, but this recipe adds moisture in a lot of clever ways that keeps these muffins from drying out quickly
- They aren't crumbly: that's right, it won't disintegrate in your hands!

I make these for a quick breakfast very regularly. It's also a great way to get my picky toddler to eat vegetables and nuts! They're also great healthy snack idea for starting and keeping New Year's resolutions! You can also check out another of my family's favorite muffins: gluten-free blackberry muffins. And if you're in the mood for a treat with deep flavors, you can also try my gluten-free matcha cookies.
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Ingredients
The secret to gluten-free baking is to add ingredients that will keep the baked goods moist. Sugars do this naturally since their hydroxyl groups form intermolecular forces with water. However, in this recipe, I wanted to reduce sugar... I replaced some with molasses which adds wonderful flavor and moisture. I am also using flaxseed meal, apples and sour cream, which all contribute to more water being retained in the batter.
Furthermore, my own gluten-free DIY all-purpose mix contains cassava flour, which is one of the highest water absorption flours out there. I also like to add pectin as my hydrocolloid, and it does wonder for moisture! Please note that while I of course recommend using my DIY mix for the above reasons, I have tested these gluten-free carrot muffins successfully with Bob Red Mill 1:1 as well as King Arthur Measure for Measure.

- Gluten-free all-purpose flour (click through for appropriate blend, including commercial options)
- Sugar & molasses
- Cinnamon
- Salt
- Baking powder
- Baking soda
- Carrots, grated
- Apple, grated
- Butter
- Milk
- Eggs
- Flaxseed meal
- Sour cream
- Optional ad-ins, like pecans and raisins
See recipe card for quantities.
Instruction

Combine all dry ingredients in a large mixing bowl. Prepare the melted butter, wet ingredients (including flaxseed meal mixed in milk) and the grated carrots/apples.

Pour the wet ingredients into the dry ingredients and mix well.

Mix until well combined. This batter is thick.

Add the carrots, apples and any desired ad-ins.

Scoop a generous amount of batter into each muffin tin.

Bake at 350F for ~25 minutes (until an inserted toothpick only has a few wet crumbs) and let cool fully.
Hint: resist the urge to take a bite of these moist savory gluten-free carrot muffins with apples as soon as these come out of the oven! I personally really don't like the texture/taste of hot carrots, and they just taste sooo much better fully cooled!
Substitutions
- Gluten-free flour - while I love using the DIY mix that I bake with for my business, you can use Bob Red Mill 1:1 or King Arthur Measure for Measure. Make sure your mix has xanthan gum. If you can't have xanthan gum, read through my hydrocolloid post for appropriate replacements.
- Sour cream - if you don't have sour cream in the fridge, you can use yogurt in a pinch!
- Dairy-free - use almond milk (or coconut milk), vegan butter and vegan yogurt.
- Egg-free - there is already a flax egg in this recipe and I do not recommend replacing the remaining eggs. I am working on specifically egg-free recipes (stay tuned), but this isn't the one!
Variations
You can add a lot of ad-ins to this recipe!
- Pecans, walnuts - add 60 grams (~¼ cup) of chopped nuts to the batter
- Raisins - add ¼ cup of raisins to the batter
- Apple sauce - you could use apple sauce instead of grated apples, but I would then omit the sour cream
Equipment
You will need basic kitchen equipment
- muffin tray
- cooling rack
- grater
- large bowl
Storage
The whole point of this recipe is to keep the savory gluten-free carrot muffins with apples moist beyond day one. That said, the muffins will keep well for up to 3 days at room temperature, covered with a tea towel. Beyond that, please freeze leftovers.
In fact, if you are the only gluten-free eater in your house and you are making these muffins for quick healthy snacks or breakfast, you could freeze all of them individually wrapped in plastic once fully cooled, for up to a month. Take out of the freezer when ready to use, and thaw to room temperature.
Top tip
I have made this gluten-free carrot muffins recipe both with freshly grated carrots, and with storebought pre-grated carrots. Do yourself a favor and grate your own carrots, it's SO much fresher tasting!
FAQ
If you want a beautiful dome on your muffins, cold ingredients are they key! It makes the center of the muffin (which is geographically speaking, the furthest area from the heat in the hot oven) bake at a different rate than the edges. The edges/top bake quickly, giving us that fat-dome!
Baking soda is a leavening agent, it's a base that will react with acidic ingredients in the batter (like apples and sour cream) and produce gases. It is used here with baking powder, and adds to the texture and taste by neutralizing acidic ingredients.
Related
Looking for other ideas for a gluten-free breakfast?


Gluten-Free Carrot Muffins with Apples
Equipment
- 1 large bowl
- 1 grater
- 1 muffin tray
- 1 cooling rack
Ingredients
Dry Ingredients
- 340 grams gluten-free all-purpose flour please click through for recommended blends
- 90 grams sugar
- 2 teaspoon baking powder
- 1 teaspoon baking soda
- 2 teaspoon cinnamon
- ½ teaspoon salt
Wet Ingredients
- 20 grams flaxseed meal
- 160 grams milk whole if possible, cold
- 60 grams molasses
- 113 grams butter non-salted, soft
- 70 grams sour cream cold
- 2 eggs cold
Add-Ins
- 200 grams carrots peeled and grated
- 70 grams apple peeled and grated
- 60 grams pecans optional, can sub other nut
- 60 grams raisins optional
Instructions
Dry Mix
- Line a muffin tin with muffin liners, and preheat the oven to 350 °F (177 °C)
- In a large mixing bowl, combine all the dry ingredients.
- Mix well.
Wet Ingredients
- Prepare the flax egg by mixing the flaxseed meal and milk together.
- If the butter is cold, microwave it in 10 second increments to soften it.
- Add the rest of the wet ingredients to the milk.
- Pour all the wet ingredients into the dry ingredients.
- Mix well. The batter will be thick.
Ad-Ins
- Add the carrots, apple, and any desired ad-ins to the batter. Mix well.
Baking
- Using a large ice cream scoop, scoop the batter equally into the muffin liners. It should be a very generous heaping spoon of thick batter.
- Place in the middle of the oven and bake for 21-26 minutes. The muffins are done when an inserted toothpick comes out with only a few moist crumbs.
- Cool fully on a cooling rack (I like to cover mine with a tea towel) before eating. Enjoy!






















Kathleen
These healthy, nutritious and delicious muffins are the perfect breakfast to start the day with.
Naelle @ GlutenFreeDIYers
Yes! We love them for breakfast too! Really filling!
Kathryn
These muffins were delicious and I love how they were filled with healthy ingredients! Will be making these again soon for my littles ones :)
Naelle @ GlutenFreeDIYers
Awesome, so glad your kiddos will get to enjoy them!
nancy
my kid loves this carrot muffin for her breakfast. Thanks for the easy recipe
Tracy
These are perfect for the kids! Love the combo of apples and carrots, such a great mom approved muffin!
Meg
It would be helpful to list all ingredients in American measures. I want to do this recipe but I got mixed up!
Naelle @ GlutenFreeDIYers
Hi Meg! For all my non-bread recipes, I give the option to use volume measurements (highlight US customary in the recipe card, next to the ingredient section).
kara couch
Such a great, easy recipe for novice gluten free bakers (like me). Easy to make, and they are guilt free. Love it! I also enjoyed the information on various flours and why it’s important to weigh then vs measure. I feel like this is my own “lesson in chemistry”. Thank you!!
Naelle @ GlutenFreeDIYers
Thanks so much! There's so much chemistry in baking, we're all little scientists :)
Meg
I found the conversion! Awesome!
Naelle @ GlutenFreeDIYers
Yay!