A healthy muffin recipe perfect for brunch, lunch boxes or a quick grab-and-go snack, these Healthy Morning Glory Muffins are made with no refined sugar or flour and plenty of healthy mix-ins. It’s truly a glorious addition to your morning!

Healthy Morning Glory Muffin Recipe

I usually am not a fan of mix-ins in baked goods.

I’m a firm believer that nuts don’t belong in brownies, raisins don’t belong in cookies, and dear goodness, what is with added chopped fruit to a delicious chocolate dessert?! Keep ’em separate!

But these morning glory muffins are where I make an exception. You get all of the best aspects of a carrot muffin and an apple muffin elevated with yummy mix-ins that help fill you up and give a delightful mix of textures. They are so incredibly satisfying, and this healthier version means you can enjoy these muffins without any guilt.

This recipe relies on a bit of honey, cinnamon and pineapple juice (or orange juice) for sweetness. There is no processed sugar needed for this recipe. I did add a small sprinkling of coconut sugar to the tops of some of the muffins to give them that classic crunch that I associate with morning glory muffins, but that’s completely optional and not necessary.

You don’t need to break out the mixer for this recipe and it’s a great one to make with the kids. It’s incredibly forgiving if they mis-measure an ingredient, make some spills, or decide to skip one of the optional mix-ins. (I’ve also listed some substitution options below so you can customize these morning glory muffins to your family’s personal preferences.)

Plus – the best part of making these with kids is that often they are so excited to eat whatever they make! 

For this recipe, I used Millican Pecan’s Pecan Pieces. I didn’t realize what a difference there could be between pecan brands, but these are so incredibly fresh and flavorful. They also have delicious snack options like the Sweet and Spicy Pecans which are perfect for the holidays. My next order, I’m trying their Pecan Butter and the Caramel Pecan Coffee! (And by the way, this is not sponsored – I just really love them.)

Why are they called Morning Glory muffins? These muffins were invented by Pam Kinstry at the Morning Glory Cafe in Nantucket in the 1970s, when trail mix and all things hippie were all the rage. She used traditional trail mix ingredients to make these muffins filling and delicious.

Can these muffins be frozen? Yes! This is one of my favorite things about baking muffins. This recipe makes about 18 muffins and we’re not going to go through them all in a few days, so I keep about half out and freeze half in an airtight freezer bag or freezer container. Then, whenever I want to pack one in Ella’s lunch, I just pull it out of the freezer in the morning, pop it in her lunch box and it’s perfect just in time for lunch! (This set of freezer containers is a crazy bargain.)

You can also microwave them for 20 seconds after pulling them out of the freezer to thaw them faster, but I prefer to just let them thaw on their own.

Looking for More Healthy Baked Goods?

Check out:

• Sugar-free Banana Bread
• Healthy Carrot Muffins
• Sugar-free Black Bean Brownies
• Chickpea Peanut Butter Blondies
• Healthy Oatmeal Cookies from Instant Oatmeal Mix

Check out our video on how to make these healthy morning glory muffins – and then don’t forget to scroll down to grab your free printable recipe card:

Healthy Morning Glory Muffin Ingredients

• Applesauce <– can use apple butter for a deeper flavor
• Egg
• Honey <– can be replaced with maple syrup
• Melted butter
• Vanilla extract
• Whole wheat flour <– can use all-purpose flour
• Baking soda
• Salt
• Cinnamon
• Orange zest <– can substitute 1 teaspoon of this shelf-stable orange peel
• Grated carrots (approximately 3 carrots)
• Pecans, chopped
• Raisins (soak for 10 minutes before adding to the recipe) <– can be replaced with another dried fruit or shredded coconut for that same chewy texture
• Apple, grated <– can replace with shredded zucchini or drained, crushed pineapple
• Pineapple or orange juice <– can use milk instead for moisture, but that will reduce the sweetness slightly

Scroll down to the printable recipe card for full measurements.

Tip: swap out any of the mix-ins (pecans, raisins, grated vegetables or apple) for your own personal preferences to make this morning glory muffin recipe truly your own.

Kitchen Tools You May Find Helpful

• Measuring cups and spoons
• Mixing bowl
• Whisk
• Muffin pan
• Muffin liners

How to Make Morning Glory Muffins

Preheat oven to 350ºF.

In a large bowl, combine the egg, applesauce, honey, melted butter and vanilla extract. Stir until fully combined. Set aside.

In a small bowl, combine the whole wheat flour, baking soda, salt, cinnamon and nutmeg.

Add the flour mixture to the wet ingredients and stir until just blended.

Add the orange zest, grated carrots, chopped pecans, raisins (soaked and drained) and grated apple to the batter and stir until well blended.

Add the pineapple or orange juice, adjusting slightly for personal preference. (I add the full amount for a tender muffin.)

Line a muffin pan with paper or silicone liners, and then portion 1/4 cup of batter into each liner.

Bake for 22-25 minutes, until an inserted toothpick comes out clean. (If they brown too much on top, place a sheet of tinfoil overtop to prevent burning.)

Let cool in the muffin pan for 2 minutes.

Best enjoyed once fully cooled.

Pin this Healthy Muffin Recipe:

Grab your free printable recipe card for our healthy morning glory muffins recipe:

These morning glory muffins are a family favorite – warm flavors, yummy mix-ins and you can feel good about serving them to your kids for a on-the-go breakfast or healthy snack.

For more healthy breakfast ideas for kids, check out our Strawberry Cheesecake Overnight Oats or our Stuffed Breakfast Sweet Potatoes.

Check out our other Breakfast Recipes here: