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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Hello! How do I adjust measurements for 6 jumbo muffins instead of 15 regular sized muffins?
This article is great and it is use to any way from the get research.
Yummy and moist muffins.
Adaptable to tastes/what you have.
I used chopped apricots, cranberries, and currants instead of raisins. Avocado oil. Grated and squeezed zucchini instead of applesauce (didn’t have any). And double the cinnamon, plus grated fresh ginger.
Delicious! Question—ground ginger was in the list of ingredients, but not in the recipe. How much should I use the next time I make these. They are sooo good!
I have made these so many times,and they are AH-MAZING!!!
Can we use egg substitute?
For example, the egg substitute from Bob’s Red Mill.
Have an allergy and would love to try these and would appreciate anyone sharing their experiences before I try it out and waste pricey ingredients in the event the egg substitute is a failure
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I love these muffins. I make them often.
I would love to make these but I’m allergic to almonds. Is there another substitute for almond flour? Thank you for the wonderful recipes you share…they are very helpful to those of us in the paleo community.
I’ve made these muffins so many times over the past few months for my morning wake up/pre-workout snack!
They are very versatile- I’ve used zucchini instead of carrots, I’ve used a banana instead of applesauce and honey. Great texture and delicious! Full of micronutrients!