Gluten-Free Paleo Morning Glory Muffins
These gluten-free Paleo Morning Glory Muffins are naturally sweetened, loaded with carrots, apples, and warm spices. Perfect gluten-free breakfast on the go!
You know what? There’s something magical about pulling a warm muffin from the oven on a chilly Sunday morning, knowing it’s packed with wholesome ingredients your whole family can enjoy. These Morning Glory Muffins (GF + Paleo) have become my go-to when I need something nourishing that doesn’t feel like “health food.”
I stumbled onto this recipe after my daughter’s soccer coach mentioned she couldn’t find a decent gluten-free breakfast muffin that actually tasted good.
Challenge accepted! After a few kitchen experiments (and one batch that resembled hockey pucks), these beauties emerged—moist, tender, and so flavorful that my kids don’t even realize they’re eating their vegetables for breakfast.
What makes these Gluten-Free Morning Glory Muffins special is how they pack grated carrots, fresh apple, warming cinnamon, and crunchy pecans into one perfectly portable package. They’re naturally sweetened with maple syrup and coconut sugar, making them a fantastic option for busy mornings or after-school snacks.
Table of Contents
Ingredients
| Ingredient | Amount |
|---|---|
| Blanched almond flour | 2 1/2 cups |
| Flaxseed meal or golden flaxseed meal | 1/2 cup |
| Baking soda | 1 tsp |
| Aluminum-free baking powder | 1 tsp |
| Ground cinnamon | 1 Tbsp |
| Fine sea salt | 1/2 tsp |
| Large eggs | 3 |
| Coconut sugar or maple sugar | 1/2 cup |
| Pure maple syrup or raw honey | 1/4 cup |
| Melted refined coconut oil | 1/4 cup |
| Unsweetened applesauce | 1/4 cup |
| Orange zest | 1 tsp |
| Orange juice | 2 Tbsp |
| Pure vanilla extract | 2 tsp |
| Grated carrots | 1 cup (about 2 large) |
| Grated apple | 1 cup (about 1 large, squeezed dry) |
| Raisins | 1/2 cup |
| Chopped pecans | 1/2 cup |
Instructions
Step 1: Preheat your oven to 350°F and line two muffin pans with 15 parchment liners. This makes cleanup a breeze and helps your Paleo Morning Glory Muffins release perfectly every time.
Step 2: In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon, and salt until well combined. Set this aside while you prepare the wet ingredients—the cinnamon will perfume your kitchen in the best way.
Step 3: In a separate mixing bowl, whisk together the eggs, coconut sugar, maple syrup, melted coconut oil, applesauce, orange zest, orange juice, and vanilla until completely smooth. The batter should look glossy and smell like sunshine! Fold in the grated carrots and apples (make sure you’ve squeezed out as much moisture as possible with paper towels), then gently stir the dry ingredients into the wet mixture until no flour spots remain.
Step 4: Fold in the raisins and pecans, distributing them evenly throughout the thick batter. Fill each muffin liner just above the top—don’t be shy, these Healthy Morning Glory Muffins need that generous dome! You’ll make 14-15 muffins total.
Step 5: Bake for 23-28 minutes, until the tops are golden brown and the centers are set. A toothpick inserted near the center should come out with just a few moist crumbs clinging to it—that’s your sign of perfectly baked muffins.
Step 6: Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins (in their liners) and continue cooling to room temperature. This resting period helps them set up beautifully and develop that tender, cake-like texture.
Substitutions
Can’t find almond flour? You can try a gluten-free all-purpose flour blend, though the texture will be slightly different and won’t be paleo-compliant. According to expert gluten-free baking research, almond flour provides healthy fats and protein that traditional flours lack.
Need a nut-free version? Swap the almond flour for sunflower seed flour in equal amounts, and replace pecans with roasted pumpkin seeds. Just know that sunflower seed flour can sometimes turn your Gluten-Free Paleo Morning Glory Muffins slightly green due to a harmless chemical reaction—they’ll still taste amazing!
Want to reduce sugar? You can cut the coconut sugar down to 1/4 cup and increase the maple syrup slightly, or use all honey if you prefer. The natural sweetness from the carrots and apples helps balance things beautifully.
No orange on hand? Lemon zest and juice work wonderfully in these Morning Glory Muffins (Gluten-Free), giving them a bright, fresh flavor. You could also try pineapple juice for a tropical twist.
Troubleshooting
Muffins turning out dense? Make sure you’re not overmixing the batter once you add the dry ingredients—gentle folding is key. Also, check that your baking powder and baking soda are fresh; expired leaveners won’t give you that beautiful rise.
Tops browning too quickly? If your oven runs hot, tent the muffins loosely with aluminum foil after 15 minutes of baking. This allows them to finish cooking through without getting too dark on top.
Batter seems too wet? This happens if you didn’t squeeze enough moisture from the grated apple. Well… lesson learned! Next time, wrap that apple in paper towels and give it a really good squeeze—you’d be surprised how much liquid comes out.
Muffins sticking to liners? Parchment liners work better than paper for these Paleo Morning Glory Muffins since they’re naturally grain-free and more delicate. Let them cool completely before peeling away the liners for best results.
Storage
Store your cooled muffins loosely covered at room temperature for the first day to maintain their tender texture. After that, transfer them to an airtight container in the refrigerator for up to 5 days—they’ll stay fresh and delicious.
For longer storage, freeze individual muffins wrapped in plastic wrap and placed in a freezer-safe bag for up to 3 months. Thaw overnight in the fridge or warm gently in the microwave for 20-30 seconds for an easy grab-and-go breakfast.
Serving Suggestions
These Healthy Morning Glory Muffins are perfect alongside your morning coffee or tea, but they’re also wonderful split and toasted with a smear of almond butter. My family loves them for Thanksgiving morning breakfast before the cooking marathon begins!
Pair them with a protein-packed smoothie or some scrambled eggs for a complete breakfast that’ll keep you satisfied until lunch. They’re also fantastic tucked into lunchboxes or enjoyed as an afternoon snack with a handful of fresh berries.
Variations
Make them dairy-free: Good news—these Gluten-Free Morning Glory Muffins are already dairy-free! Just make sure your chocolate chips are dairy-free if you decide to add them as a fun variation.
Kid-friendly version: If your little ones aren’t fans of raisins, swap them for mini chocolate chips or dried cranberries. You can also reduce the cinnamon slightly if they prefer a milder spice flavor.
Boost the protein: Add 2 tablespoons of collagen peptides or your favorite unflavored protein powder to the dry ingredients. This makes them even more filling without changing the texture—I do this when I know we’ll be running around all morning.
Tropical twist: Replace the raisins with unsweetened shredded coconut and the pecans with macadamia nuts for a vacation-worthy flavor. Add a touch of pineapple juice instead of orange for extra island vibes!
Gluten-Free Paleo Morning Glory Muffins FAQs
Can I make these muffins egg-free?
Unfortunately, eggs provide crucial structure in these Paleo Morning Glory Muffins, and I haven’t found a substitute that works as well. The three eggs bind all those wonderful mix-ins together beautifully.
How do I prevent the mix-ins from sinking?
Tossing your raisins and pecans in a tiny bit of almond flour before folding them in helps suspend them throughout the batter. The thick batter itself does most of the work, though!
What’s the best way to grate the carrots and apple?
I use the large holes on a box grater for perfect texture in these Morning Glory Muffins (GF + Paleo). A food processor works too, but pulse carefully—you want shreds, not mush!
Can I double this recipe?
Absolutely! This recipe doubles beautifully for meal prep or freezer stocking. Man, oh man, having a stash of these in your freezer makes busy weekday mornings so much easier.
Why squeeze the grated apple?
Apples contain a surprising amount of water that can make your Gluten-Free Paleo Morning Glory Muffins soggy. Squeezing out excess moisture ensures perfectly tender (not wet) muffins every single time.
Looking for more wholesome muffin inspiration? Check out my naturally sweetened lemon poppy seed muffins for bright citrus flavor, or try these cozy pumpkin spice muffins when fall rolls around. And if you love the apple-cinnamon combo as much as I do, you’ll adore these tender apple cinnamon breakfast muffins!
These Morning Glory Muffins (Gluten-Free) prove that healthy baking doesn’t have to be complicated or bland. With simple, wholesome ingredients and a little love, you can create nourishing treats that make everyone at your table smile. Happy baking, friend!
Gluten-Free Paleo Morning Glory Muffins
Equipment
- 2 muffin pans
- Parchment muffin liners
- Large mixing bowl
- Separate mixing bowl
- Whisk
- Box grater
- Paper towels
- Wire cooling rack
- Toothpick
Ingredients
Dry Ingredients
- 2 ½ cups blanched almond flour
- ½ cup flaxseed meal or golden flaxseed meal
- 1 tsp baking soda
- 1 tsp aluminum-free baking powder
- 1 Tbsp ground cinnamon
- ½ tsp fine sea salt
Wet Ingredients
- 3 large eggs
- ½ cup coconut sugar or maple sugar
- ¼ cup pure maple syrup or raw honey
- ¼ cup melted refined coconut oil
- ¼ cup unsweetened applesauce
- 1 tsp orange zest
- 2 Tbsp orange juice
- 2 tsp pure vanilla extract
Mix-Ins
- 1 cup grated carrots about 2 large
- 1 cup grated apple about 1 large, squeezed with paper towels to remove excess water
- ½ cup raisins
- ½ cup chopped pecans
Instructions
- Preheat your oven to 350°F and line two muffin pans with 15 parchment liners. This makes cleanup a breeze and helps your Paleo Morning Glory Muffins release perfectly every time.
- In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon, and salt until well combined. Set this aside while you prepare the wet ingredients—the cinnamon will perfume your kitchen in the best way.
- In a separate mixing bowl, whisk together the eggs, coconut sugar, maple syrup, melted coconut oil, applesauce, orange zest, orange juice, and vanilla until completely smooth. The batter should look glossy and smell like sunshine! Fold in the grated carrots and apples (make sure you’ve squeezed out as much moisture as possible with paper towels), then gently stir the dry ingredients into the wet mixture until no flour spots remain.
- Fold in the raisins and pecans, distributing them evenly throughout the thick batter. Fill each muffin liner just above the top—don’t be shy, these Healthy Morning Glory Muffins need that generous dome! You’ll make 14-15 muffins total.
- Bake for 23-28 minutes, until the tops are golden brown and the centers are set. A toothpick inserted near the center should come out with just a few moist crumbs clinging to it—that’s your sign of perfectly baked muffins.
- Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins (in their liners) and continue cooling to room temperature. This resting period helps them set up beautifully and develop that tender, cake-like texture.
