The Best Morning Glory Muffins (Gluten-Free)

Name: The Best Morning Glory Muffins (Gluten-Free)
Prep time: 10 min
Cook time: 30 min
Total time: 40 min
Ingredients: 1 cup grated zucchini (don't squeeze out liquid (measure after grating)); 1 cup grated carrot; 1/2 cup grated apple; 1/3 cup mashed banana; 1/3 cup butter (or coconut oil, melted); 1/4 cup honey (or maple syrup); 2 eggs (flax eggs will also work); 2 tsp vanilla extract; 1¾ cup gluten free all-purpose flour (with xanthan gum - or use regular all-purpose flour); 1/4 cup unsweetened coconut flakes (or rolled oats); 1 tsp baking soda; 1 tsp cinnamon; 1/4 tsp sea salt; 1/2 cup chocolate chips (or chopped nuts); 1/2 cup raisins (or dried cranberries, chopped dates, or other dried fruits)

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Gluten-free morning glory muffins on a wire cooling rack.

Why You’ll Love This Recipe

This gluten-free morning glory muffins recipe is such a hearty and delicious breakfast, and they’re great on-the-go (just like my reader favorite healthy sweet potato muffins). This is one of my favorite ways to pack extra veggies into my kids’ meals, and both of them absolutely love these muffins. That’s always my litmus test for a breakfast recipe worth keeping in regular rotation.

They’re also freezer-friendly, which makes them ideal for emergency breakfasts or snacks. I try to keep a batch on hand at all times because they reheat beautifully and feel just as satisfying as the day they were baked.

If you love muffins that feel nourishing but still taste like a treat, you’ll also like these apple muffins with bacon, which have that same cozy, fruit-forward breakfast feel.

Ingredients You’ll Need

Gluten-free morning glory muffins recipe ingredients labeled and laid out on a gray countertop.

Grated zucchini: Adds moisture without making the muffins taste vegetal.
Grated carrot: Brings natural sweetness and that classic morning glory texture.
Grated apple: Adds brightness and helps keep the crumb tender.
Mashed banana: Contributes sweetness and structure.
Butter: Gives richness and flavor. You can sub coconut oil instead if preferred.
Honey: Provides gentle sweetness without overpowering the other ingredients. Can sub maple syrup.
Eggs: Bind everything together. Flax eggs will also work.
Vanilla extract: Helps round out the flavors.
Gluten-free all-purpose flour blend with xanthan gum: Helps the muffins hold together and stay moist instead of crumbly. You can also use regular all-purpose flour.
Unsweetened coconut flakes: Add texture, though rolled oats work just as well if that’s what you have on hand.
Baking soda: Helps the muffins rise.
Cinnamon: Adds warmth.
Sea salt: Balances the sweetness.
Chocolate chips: Add little pockets of sweetness throughout the muffins, making them especially appealing to kids. You can also use chopped nuts to add richness and crunch.
Raisins: Bring a chewy texture and a burst of sweetness. You can use other dried fruits if desired. This flexibility is what makes these morning glory muffins easy to adapt based on what you already have.

How to Make Gluten-Free Morning Glory Muffins

A large wooden bowl with zucchini, carrot, apple, banana, butter, honey, eggs, and vanilla extract.

Step 1: Preheat the oven to 350°F. Line a 12-cup muffin tin with liners and lightly spray with cooking spray. In a large bowl, stir together the zucchini, carrot, apple, banana, butter, honey, eggs, and vanilla extract until well combined.

A white bowl with gluten-free flour, coconut flakes, baking soda, cinnamon, and sea salt mixed together.

Step 2: In a separate bowl, whisk together the gluten-free flour, coconut flakes, baking soda, cinnamon, and sea salt.

Dry ingredients being added to the wet ingredients.

Step 3: Add the dry ingredients to the wet ingredients and mix gently until just combined, leaving a few streaks of flour.

Chocolate chips and raisins being folded into the batter.

Step 4: Fold in the chocolate chips and raisins until evenly distributed.

Batter being divided evenly among the muffin cups, filling them almost to the top.

Step 5: Divide the batter evenly among the muffin cups, filling them almost to the top. Bake for 27-30 minutes, until a toothpick inserted in the center comes out with just a few crumbs.

Gluten-free morning glory mufins on a wire cooling rack.

Step 6: Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.

Customization & Mix-In Options

These healthy morning glory muffins are easy to customize depending on what you have on hand. If you prefer not to use chocolate chips, nuts like pecans, walnuts, or pumpkin seeds work well. You can also swap the raisins for dried cranberries, chopped dates, or any dried fruit you like.
If you enjoy baking with warm spices, apples, and naturally sweet ingredients, you might also love this apple cinnamon bread, which uses many of the same cozy flavors and works well as another make-ahead breakfast option.

Close-up of a gluten-free morning glory muffin broken in half.

Storage & Freezer Tips

These muffins store exceptionally well, which is why they’re such a good make-ahead breakfast option. You can keep them in an airtight container in the fridge for up to 5 days, or freeze them for up to 3 months.
I like to freeze them once fully cooled, then thaw overnight in the fridge or warm briefly before serving.
To save time during prep, you can grate the vegetables and apples using a box grater, but I often use a food processor with a shredder attachment to make things faster and less messy.

Recipe FAQs

Are these morning glory muffins healthy?

Morning glory muffins are a more wholesome muffin option thanks to ingredients like carrots, fruit, and nuts, which add fiber and make them more filling. They’re not overly sweet and work well as a balanced breakfast or snack.

What is the best gluten-free flour to use for morning glory muffins?

A gluten-free all-purpose flour blend with a built-in binder like xanthan gum works best. These blends provide the structure needed for soft, tender muffins without a dense texture.

What makes morning glory muffins different from regular muffins?

Morning glory muffins are heartier than regular muffins and include a mix of fruits, vegetables, warm spices, and add-ins, making them more filling and less dessert-like.

Can I make these morning glory muffins dairy-free?

Yes. You can swap the butter for a dairy-free butter alternative that’s suitable for baking with similar results.

These gluten-free morning glory muffins are the kind of recipe that quietly becomes a staple (just like my lemon blueberry muffins) – dependable, nourishing, and easy to keep on hand. Whether you’re baking for busy mornings, kids’ breakfasts, or freezer prep, they fit right into everyday life.