A Muffin You’ll Feel Good Eating!
These easy-to-make, moist whole wheat morning glory muffins are wholesome, flavorful, and packed with ingredients you’ll feel good eating. They have a tender crumb and a slightly dense texture, making them a hearty and delicious breakfast option.
Why You’ll Love These Muffins
These Whole Wheat Morning Glory Muffins are a delightful blend of warm spices, natural sweetness, and satisfying texture. Packed with shredded carrots, juicy apple, crunchy nuts, chewy raisins, and a touch of coconut, they deliver the perfect balance of flavor and a daily dose of fruits, veggies, and nuts. Think of them as a cross between carrot cake and a hearty breakfast muffin—slightly sweet, warmly spiced, and incredibly satisfying.
This version is inspired by the beloved Whole Foods Morning Glory Muffin but with a homemade twist. They’re naturally sweetened with honey or maple syrup and made with whole wheat flour.
For more delicious homemade muffins, try my double chocolate zucchini muffins, these light and fresh lemon poppy seed muffins, or my kids’ personal favorite, these chocolate chip banana muffins next! It’s the reason we always intentionally have bananas rotting away on the counter.

Ingredients You’ll Need:
- Whole wheat flour – Adds fiber and a slightly nutty flavor.
- Baking soda & baking powder – Helps the muffins rise.
- Cinnamon – Warm, cozy spices that enhance the flavors.
- Salt – Balances the sweetness and enhances flavor.
- Carrots – Grated for moisture and natural sweetness.
- Apple – Adds a touch of sweetness and keeps the muffins tender.
- Unsweetened coconut flakes – Provides texture and a mild tropical note.
- Raisins – Adds natural sweetness and chewiness.
- Walnuts or pecans – For crunch and a boost of healthy fats.
- Eggs – Helps bind the ingredients and provide structure.
- Canola oil – Adds moisture and richness.
- Vanilla extract – Enhances the overall flavor.
Ingredient Substitutions
If you’d like to make these gluten-free, substitute whole wheat flour with a 1:1 gluten-free flour blend. I like Bob’s Red Mill!
Not a fan of raisins? Feel free to swap them out for dried cranberries, chopped dates, or even mini chocolate chips.

Directions
Full instructions and ingredient list can be found in the recipe card below.
- Preheat the oven to 350°F. Line a muffin tin with paper liners or grease well.
- Whisk dry ingredients. In a large bowl, whisk together the whole wheat flour, baking soda, baking powder, cinnamon, kosher salt, and ground walnuts.
- Mix wet ingredients. In another bowl, whisk together the eggs, canola oil, and vanilla extract.
- Combine. Gently fold the wet ingredients into the dry, then stir in the shredded carrots, apple, coconut, and raisins.
- Scoop and bake. Divide the batter evenly among the muffin cups, sprinkle with remaining nuts or shredded coconut flakes (optional), then bake for 22-25 minutes, or until a toothpick inserted in the center comes out clean.
- Cool and enjoy. Let the muffins cool for a few minutes before transferring to a wire rack.
Serving Suggestions
Enjoy warm with a smear of butter or cream cheese, or pair with a cup of coffee or tea for a satisfying breakfast. Honestly, I’m team muffin as a mid-day snack, so don’t limit yourself to enjoying them solely at breakfast!

Make-Ahead, Storage & Freezing
- Make-Ahead: These muffins can be made in advance and stored for easy grab-and-go breakfasts.
- Storage: Store in an airtight container at room temperature for up to 3 days or in the fridge for up to a week.
- Freezing: Freeze individually wrapped muffins in a freezer-safe bag for up to 3 months. Reheat in the microwave or oven as needed.

If you make these Whole Wheat Morning Glory Muffins, I’d love to hear how they turned out! Leave a review and let me know what you think. Happy baking!
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Rate this Recipe35-Minute Whole Wheat Morning Glory Muffins
Equipment
Ingredients
- 1½ cups whole wheat flour
- ½ cup granulated sugar
- ½ cup dark brown sugar
- 1½ tsp baking soda
- 1½ tsp ground cinnamon
- ¼ tsp Kosher salt
- ½ cup + 2 Tbsp walnuts, finely ground
- 3 large eggs
- ⅔ cup canola oil
- 1 tsp pure vanilla extract
- 1 medium apple, (about ~½ cup apple) peeled, cored, and grated
- 1 cup carrots, shredded
- ½ cup raisins
- ¼ cup toasted coconut flakes
Instructions
- Mix dry ingredients. Preheat oven to 350°F and line a standard muffin pan with muffin liners. In a large bowl, combine 1½ cups whole wheat flour, ½ cup brown sugar, ½ cup granulated sugar, 1½ tsp baking soda, 1½ tsp cinnamon, ¼ tsp Kosher salt, and ½ cup crushed walnuts. Whisk to combine.
- Mix wet ingredients, then combine with dry. In a separate bowl, whisk together 3 large eggs, ⅔ cup canola oil, and 1 tsp vanilla extract. Pour wet ingredients into dry ingredients and fold gently until just barely combined.
- Fold in remaining ingredients. Add ½ cup grated apple, 1 cup shredded carrots, ½ cup raisins, and ¼ cup coconut flakes, then mix a few more times, just to incorporate. Fill each muffin tin about ⅔ full, then sprinkle each with the remaining crushed walnuts.
- Bake the muffins. Bake until a toothpick inserted in the center comes out clean, about 22-25 minutes. The muffins will appear dark in color from the whole wheat flour. Transfer to a wire rack to cool, then enjoy!
Notes
- Storage: Store in an airtight container at room temperature for up to 3 days or in the fridge for up to a week.
- To freeze muffins: cook and allow to cool completely, then store in an airtight, freezer-safe container and place in freezer. Muffins will keep up to 3 months.


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