
This hearty Morning Glory Muffin recipe transforms humble pantry ingredients into a wholesome breakfast treat packed with fruits, vegetables, and whole grains. These cinnamon-spiced muffins strike the perfect balance between apple cake, spice cake, and moist carrot cake while providing nourishment to start your day.
I first discovered morning glory muffins when looking for ways to sneak more vegetables into my family's breakfast routine. What started as a nutrition experiment quickly became our favorite weekend ritual, with everyone gathering in the kitchen to help grate carrots and apples.
Ingredients
- Whole wheat flour: Provides hearty texture and nutty flavor while adding more fiber than all purpose
- Baking soda: Ensures these dense, ingredient-packed muffins rise beautifully
- Ground cinnamon and ginger: Create the signature warm spice profile these muffins are known for
- Brown sugar: Adds moisture and depth of flavor beyond what regular sugar provides
- Honey: Contributes natural sweetness and helps preserve freshness
- Oil: Keeps the muffins tender and moist for days
- Applesauce: Reduces the need for excess fat while adding natural sweetness
- Orange juice: Brightens the flavor and activates the baking soda for proper rising
- Carrots and apples: Provide moisture, natural sweetness, and nutritional benefits
- Raisins: Add chewy texture and concentrated fruit flavor in every bite
- Pecans: Contribute essential crunch and healthy fats to balance the texture
Step-by-Step Instructions
- Prep Your Equipment:
- Preheat your oven to 425°F and prepare your muffin pans with nonstick spray or liners. The recipe makes 14 to 16 muffins, so you will need either two pans or plan to bake in batches. Make sure to spray the tops of the muffin pans too, as these muffins will rise significantly.
- Mix Dry Ingredients:
- Whisk together the whole wheat flour, baking soda, cinnamon, ginger, salt, and optional flaxseed in a large bowl until thoroughly combined. This step is crucial for evenly distributing the leavening and spices throughout the batter.
- Combine Wet Ingredients:
- In a separate medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce, orange zest, orange juice, and vanilla until smooth and well blended. The mixture should look uniform with no streaks of egg visible. Fold in the shredded carrots and apples, making sure they are evenly distributed.
- Create The Batter:
- Pour the wet ingredient mixture into the dry ingredients. Using a wooden spoon or rubber spatula, gently fold everything together with just a few strokes. When the mixture is partially combined, add the raisins and pecans and continue folding just until no dry pockets of flour remain. Overmixing will develop gluten and create tough muffins.
- Fill And Bake:
- Spoon the batter into the prepared muffin cups, filling them completely to the top. This generous filling creates those beautiful domed muffin tops. Bake at 425°F for exactly 5 minutes, then without opening the oven, reduce the temperature to 350°F and continue baking for 18 more minutes until a toothpick inserted in the center comes out clean.
- Cool And Store:
- Allow the muffins to cool in the pan for 10 minutes before transferring to a wire rack to cool completely. This resting period ensures they set properly and won’t fall apart when removed from the pan.

The addition of flaxseed is my favorite nutritional boost in this recipe. My grandmother always added it to her baked goods, claiming it was her secret to longevity. Whether that's true or not, I love carrying on her tradition and knowing I'm adding heart-healthy omega-3s to our breakfast.
Mastering The Perfect Texture
The secret to these muffins' perfect texture lies in the initial high-temperature bake. Starting at 425°F creates an immediate rise that forms those bakery-style domed tops everyone loves. When you reduce the temperature, the interiors can finish cooking without burning the exteriors. This technique works with almost any muffin recipe and creates professional-looking results every time.
Make-Ahead Options
These muffins are perfect for meal prepping. The batter can be prepared the night before and refrigerated. Just give it a gentle stir in the morning before baking. Alternatively, bake a double batch and freeze the extras. Wrap each cooled muffin individually in plastic wrap, then store in a freezer bag for up to 3 months. Thaw overnight in the refrigerator or defrost in the microwave for about 30 seconds when you need a quick breakfast.
Seasonal Variations
- Winter: Substitute dried cranberries for raisins and add 1/2 teaspoon of nutmeg for a holiday spin
- Spring: Add 1/2 cup fresh blueberries and lemon zest instead of orange
- Summer: Include 1/2 cup diced peaches and use almond extract instead of vanilla
- Fall: Add 1/2 cup pumpkin puree in place of some applesauce and increase the cinnamon to 1 tablespoon

Frequently Asked Questions
- → What makes morning glory muffins healthy?
These muffins include whole wheat flour, carrots, apples, raisins, and flaxseed, offering fiber, vitamins, and natural sweetness.
- → Can I substitute ingredients in morning glory muffins?
Yes, you can use alternatives for oils, sweeteners, and add-ins like nuts or raisins. Check the detailed substitution suggestions above.
- → How do I store leftover muffins?
Store muffins in an airtight container at room temperature for 2 days or refrigerate for up to 1 week. They also freeze well for 3 months.
- → Why bake muffins at a high initial temperature?
The high temperature helps muffins rise quickly, creating tall tops, before baking at a lower temperature to cook through.
- → Can I make these muffins without eggs?
You can replace eggs with flaxseed or chia seed eggs, mashed bananas, or yogurt as alternative binders.