These Paleo Morning Glory Muffins are perfect for breakfast and snacking! Loaded with goodies like apples, carrots, raisins and pecans and flavored with orange zest, these tender and moist muffins absolutely delicious, healthy, gluten free, grain free, dairy free, and refined sugar free.

Morning glory muffins really have the best of everything when it comes to muffins!
Fruit + veggies, warm spices, moist, tender, and healthy!
They’re the best combination of my apple muffins, orange pecan muffins and carrot cake.
Hmmm, does that sound just a little bit strange? Let me tell you – it’s delicious!
The orange zest combined with the raisins and pecans is soooo good.
The apple and carrot make the muffins moist but definitely not TOO moist (as paleo muffins can sometimes be).
Whether you grab one for breakfast or a snack, they’re the perfect grain free bite to satisfy a sweet tooth.

What You Need to Make 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.
Store muffins at room temperature for the first day (loosely covered) then in the refrigerator for up to 5 days. Enjoy!

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.

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!
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!
Paleo Morning Glory Muffins {Gluten Free, Dairy Free}

Paleo Morning Glory Muffins {Gluten-Free, Dairy-Free}

Ingredients
- 2 1/2 cups blanched almond flour
- 1/2 cup flaxseed meal or golden flaxseed meal
- 1 tsp baking soda
- 1 tsp aluminum free baking powder
- 1 Tbsp ground cinnamon
- 1/2 tsp fine sea salt
- 3 large eggs
- 1/2 cup coconut sugar or maple sugar
- 1/4 cup pure maple syrup or raw honey
- 1/4 cup melted refined coconut oil
- 1/4 cup unsweetened applesauce
- 1 tsp orange zest
- 2 Tbsp orange juice
- 2 tsp 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
-
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. 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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Want More Paleo Muffin Recipes? Try One of These!
Cranberry Orange Pecan Muffins
Blueberry Muffins with Almond Streusel
Cinnamon Raisin Sweet Potato Muffins
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Followed the recipe exactly and these are INCREDIBLE!!! Wow, wow, wow! 5 stars!!
Made the muffins and they turned out great. Anyone know if I could substitute zucchini for the carrot or apple? Thanks.
Could this be turned into bread?
I typically don’t comment if I have made changes to the recipe, but since running out to the store is not as fun as it used to be and we are all making do with what we have as much as possible, I thought I would share my success story. I subbed the applesauce for butternut squash purée, 1 smallish carrot, added ginger & used raisins, almond and apricots as the mix-ins. So good! Moist, but not the weird custardy consistency you sometimes get with too much liquid in paleo baking. Or at least I have gotten. Definitely a good mix up for breakfast muffins!
these muffins are amazing! I”ve made them a dozen times already–they are always excellent! I agree with squeezing out as much of the liquid as possible from apples and carrots.
Hi! I have a question about the recipe — is there any way to reduce the sugar without compromising the texture? Could I maybe sub in a mashed ripe banana for the maple syrup? Thanks!
I’ve made these twice now. First with the full amount of coconut sugar and maple syrup, and the second time with 1/2 the suggested amounts of both sweeteners. My preference is for the lower sugar but they were both awesome. I added a tablespoon of micro-planed ginger and 2 tablespoons of water the second time to offset the liquid from the maple syrup. They turned out great.
I also used homemade rhubarb sauce instead of applesauce because I didn’t have the applesauce. Great recipe. I gave some as gifts and everyone raved about them.
Hi, I would really like to try these but I cant find flaxseed meal where I am staying, is there an alternative. Thanks.
I consider myself a bit of a morning glory muffin connoisseur and this is the best recipe I’ve found yet! I’ve also never left a comment on a recipe before but they’re that good.
We love these muffins. I’m considering making a double batch and baking in 9” pans for a carrot cake for Easter dessert (making a swerve cream cheese frosting). I’m hoping it works in this form!
These are amazing!! I used craisins and subbed 1/4 honey instead of the coconut sugar. I will be making these often!!