These paleo morning glory muffins are soft, perfectly spiced and packed with shredded carrots, apple, orange and nuts for the best texture and flavor. These gluten free and paleo muffins are easy to make, perfect for breakfast and freezer-friendly!
*Originally published in August 2020. Updated April 2026 with helpful tips and additional step-by-step information for the best results.
Morning glory muffins really have the best of everything when it comes to muffins!
Fruit + veggies, warm spices, moist, tender, and healthy!
If you love bakery-style muffins but want something made with simple, wholesome ingredients, these healthy morning glory muffins are about to become a favorite.
They’re soft, perfectly spiced and packed with shredded carrots, apple, orange, and nuts for the best texture and flavor.
Made with almond flour and naturally sweetened, these gluten free and paleo muffins are perfect for meal prep, quick breakfasts or an easy snack that actually keeps you full.
They have everything you love about classic morning glory muffins, but with a better-for-you twist!
If you’ve been looking for a paleo muffin recipe that’s hearty, flavorful and easy to make, these morning glory muffins are a must-try. They have everything you love about classic bakery-style muffins, but made with wholesome ingredients you can feel good about!
Why you’ll love these morning glory muffins
These muffins are easy to make, naturally sweetened, perfect for meal prep and make a great option if you’re searching for healthy muffins made with almond flour that stay soft for days!
They’re freezer friendly too! Let’s get into the details so you can make them ASAP!
What are morning glory muffins?
Morning glory muffins are hearty, fruit- and vegetable-packed muffins traditionally made with carrots, apples, coconut, nuts and warm spices. They’re known for their moist texture and naturally sweet flavor.
Are morning glory muffins healthy?
They can be, depending on the ingredients. These healthy morning glory muffins are made with almond flour, naturally sweetened and packed with whole ingredients, making them a more balanced option than traditional bakery versions.
How to make morning glory muffins with almond flour
Using almond flour keeps these muffins soft and moist while adding healthy fats and protein. The key is balancing it with ingredients like eggs and a small amount of starch (like tapioca) to help them rise and hold their structure.
What you need to make these paleo morning glory muffins
This recipe is loaded with real-food goodies! Which DOES mean there are a few more ingredients in here than many of my muffin recipes.
But well worth it for the nutrition AND flavor.
Here’s what you’ll need to prepare the muffins:
- blanched almond flour
- flaxseed meal or golden flaxseed meal
- baking soda
- baking powder
- ground cinnamon
- ground ginger
- fine sea salt
- eggs
- maple sugar or coconut sugar
- pure maple syrup or raw honey
- refined coconut oil
- unsweetened applesauce
- orange zest
- fresh orange juice
- pure vanilla extract
- grated carrots
- grated apple
- raisins
- pecans
How to Make Paleo Morning Glory Muffins
Preheat your oven to 350° F and line 2 muffins pans with 15 parchment liners. In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon and salt, set aside.
In a separate mixing bowl, whisk together the eggs, sugar, syrup or honey, coconut oil, applesauce, orange zest and juice and vanilla until smooth.
Fold in the grated carrots and apples (after squeezing out as much water as possible) then gently stir the dry ingredients into the wet until no flour spots show.
Fold in the raisins and pecans, then fill the muffin liners just above the top, (batter will be thick). You will make 14-15 muffins.
Bake for 23-28 minutes, until golden brown on top and set in the center. A toothpick inserted near the center of a muffin should come out with a few crumbs.
Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins from the pan (in their liners) and continue to cool to room temperature.
What makes these paleo muffins so moist?
The combination of grated apple, shredded carrots and eggs creates a naturally moist texture without needing excess oil. Almond flour also helps retain moisture, keeping the muffins soft even after storing.
Can I make these muffins without refined sugar?
Yes! These muffins are naturally sweetened with maple sugar (or coconut sugar), making them free from refined sugars while still tasting perfectly sweet.
How to store and freeze morning glory muffins
Store the muffins in an airtight container at room temperature for up to 2 days, or refrigerate for up to 5 days. For longer storage, freeze them individually and thaw as needed for a quick breakfast or snack.
Tips for the Perfect Paleo Morning Glory Muffins
Paleo baked goods can get soggy – yes, it’s true! Especially when baking with fruits and veggies.
Because the flours used are high in fat and can be dense, even a little bit of extra water from ingredients can weigh the muffins down and create a less than ideal level of moistness – ugh – not my favorite!
Since you have carrots, apples and applesauce in this recipe you need to be extra careful about removing excess moisture from the apples and carrots.
Don’t just drain on paper towels, make sure you squeeze out as much water as possible before adding to the batter.
Grain Free Baking Powder
Now, for baking powder! I am okay to use an aluminum free baking powder, which is not technically paleo due to the corn starch.
If you want to make your own grain free and paleo version, it’s actually really easy.
Simply mix 1 tsp baking soda with 2 tsp cream of tartar.
For this recipe, you will need just 1 tsp total of this mixture.
FAQ for Morning glory muffins
Can I make these nut-free?
Since almond flour is the base, these are not nut-free. For a nut-free version, you would need a different recipe using a seed-based or gluten free flour blend.
Can I use a different sweetener?
Yes, coconut sugar works well in place of maple sugar. To use only maple syrup, you would need to add about 1/4 cup more almond flour to adjust for the excess moisture.
Why did my muffins not rise?
This can happen if the batter is overmixed or if the baking soda isn’t fresh. Letting the batter rest briefly before baking can also help improve texture.
Can I make these into mini muffins?
Yes! Reduce the baking time to about 12–15 minutes and check for doneness early.
Storing Paleo Morning Glory Muffins
I kept my muffins out on the countertop, loosely covered, for the first day and they were perfect. After that, I placed them in a sealed container and kept them in the refrigerator for the next few days.
They should last up to 5 days in the refrigerator. I like to pop them in the toaster oven to warm them up a little after they’ve been refrigerated.
They’re so good with a little extra ghee or grass-fed butter and honey!
Ingredient Substitutions and Variations
Almond Flour
Almond flour gives these muffins their soft, moist texture and rich flavor.
Replace with:
- There isn’t a direct 1:1 substitute for almond flour in this recipe
- A gluten free flour blend may work, or gluten free oat flour, but results will vary and texture will be different
Flaxseed Meal or Golden Flaxseed Meal
Replace flaxseed with an equal amount of blanched almond flour for a similar result.
Maple Sugar
Adds natural sweetness without refined sugar.
Replace with:
- Coconut sugar (1:1 swap)
- Brown sugar (not paleo, but works perfectly)
Refined Coconut Oil
Provides moisture and richness.
Replace with:
- Melted butter (if not dairy-free)
- Avocado oil (for a more neutral flavor)
Shredded Carrots
A key ingredient for texture and moisture.
Replace with:
- No true substitute — best to keep
- You can slightly reduce the amount if preferred
Shredded Apple
Adds natural sweetness and moisture. You can replace with shredded zucchini or more shredded carrot. I also love replacing the 1 cup of shredded apple with 2/3 cup canned crushed pineapple (drained).
Applesauce
If needed, replace with apple butter, mashed banana, canned crushed pineapple (drained), or pumpkin puree.
Orange Zest and Juice
Replace with additional applesauce or almond milk.
Pecans
Replace with: Sunflower seeds or pumpkin seeds (nut-free option). Omit for a softer muffin or add shredded coconut for texture
Raisins
Add sweetness and chewiness. Replace with chopped dates, dried cranberries, or omit for lower sugar
*If making multiple substitutions, try to keep:
- The wet-to-dry ratio similar
- At least one moisture-rich ingredient (apple, carrot, or oil)
This ensures your muffins stay soft and don’t dry out!
These healthy morning glory muffins are the perfect balance of cozy, nourishing and easy to make.
Whether you’re baking for the week ahead or just want a satisfying breakfast you can grab and go, they’re a recipe you’ll come back to again and again.
I hope you’re ready for a delicious addition to your mornings with these paleo morning glory muffins! Grab your ingredients and preheat your oven – it’s time to bake!
If you try them, let me know in the comments – I love hearing how you customize them!
Want More Paleo Muffin Recipes? Try One of These!
Cranberry Orange Pecan Muffins
Healthy Morning Glory Muffins (Almond Flour, Gluten Free, Paleo)
If you love bakery-style muffins but want something made with simple, wholesome ingredients, these healthy morning glory muffins are about to become a favorite. They’re soft, perfectly spiced and packed with shredded carrots, apple, orange raisins and nuts for the best texture and flavor.
Ingredients
- 2 1/2 cups blanched almond flour
- 1/2 cup flaxseed meal or golden flaxseed meal
- 1 teaspoon baking soda
- 1 teaspoon baking powder aluminum free
- 1 tablespoon ground cinnamon
- 1/2 teaspoon fine sea salt
- 3 large eggs
- 1/2 cup maple sugar or coconut sugar
- 1/4 cup pure maple syrup or raw honey
- 1/4 cup refined coconut oil melted
- 1/4 cup unsweetened applesauce
- 1 teaspoon orange zest
- 2 tablespoon orange juice
- 2 teaspoons pure vanilla extract
- 1 cup grated carrots about 2 large
- 1 cup grated apple about 1 large, squeezed with paper towels to remove excess water
- 1/2 cup raisins
- 1/2 cup chopped pecans
Instructions
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Preheat your oven to 350° F and line a muffin pan with parchment liners. This recipe makes 14 muffins so plan to bake them in 2 batches, or line 2 muffin pans if you have room in your oven.
-
In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon and salt, set aside.
-
In a separate mixing bowl, whisk together the eggs, sugar, syrup or honey, coconut oil, applesauce, orange zest and juice and vanilla until smooth. Fold in the grated carrots and apples (after squeezing out as much water as possible) then gently stir the dry ingredients into the wet until no flour spots show.
-
Fold in the raisins and pecans, then fill the muffin liners just above the top, (batter will be thick) to make 14 muffins. Bake for 23-28 minutes, until golden brown on top and set in the center. A toothpick inserted near the center of a muffin should come out with a few crumbs.
-
Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins from the pan (in their liners) and continue to cool to room temperature. Store muffins at room temperature for the first day (loosely covered) then in the refrigerator for up to 5 days. Enjoy!
Nutrition
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Loved this! So delish! Wasn’t sure how the Orange would be but turned out great.
Love the combo of orange zest grated apple and grated carrot! Tastes great but has trouble holding together. They get messy and crumbly quick. Refrigerating does help. Thanks for sharing/creating! One of my sons is grain free and I love finding baked goods I can feed him. Scaled way back on maple syrup and only added half of recommended coconut sugar. I subbed walnut, butter and coconut flour for the pecans, coconut oil and flaxseed meal and all turned out just fine. Anyone try to do this completely vegan?
Does anyone have any substitution suggestions for the apple sauce?
I used banana instead!
Just ate one warm from the oven because I couldn’t wait. 🙂 Delicious flavor! I made a half batch and used two eggs, went the maple syrup route, and had to used cane sugar because I didn’t have another option. They didn’t rise as much as I hoped, but they’re not stodgy in texture like a lot of gluten-free cakes. My favorite part is the crusty top, so next time I may try baking in a pan to get more surface area, and also will give it a little more time. (I stopped at 25 minutes.) Thanks for the recipe!! <3
These muffins look so tasty. Amazing, I will surely gonna try it out.
Very tasty! & healthy ingredients
Absolutely delicious!!!
Only thing I changed was changed the coconut sugar to monk fruit ( cut the amount in half)
Will definitely be making again
Yummy
These are the best muffins I’ve ever had! So good!
Very good!! Gonna even put less honey in next time (I added chopped dates for sweetness) and more nuts…yummy!