These healthy whole wheat morning glory muffins are such a treat to wake up to! They’re filled with good-for-you ingredients like shredded apples, carrots, and raisins.

Whole Wheat Morning Glory Muffins - Daisybeet

Have you ever had a morning glory muffin? They’re not as common to find in bakeries, but if you see one, grab it! Or, you can make a batch of these healthy muffins.

Morning glory muffins are packed to the brim with yummy ingredients, including shredded carrots, apples, nuts, and dried fruit. My version is made with whole wheat flour, KORU apples, walnuts, and golden raisins. They’re just sweet enough, and spiced with cinnamon and cardamom.

KORU apples are one of my favorite apple varieties! They’re delicious and super crunchy to eat on their own. But, they also taste amazing in baked goods, thanks to hints of vanilla and spice in their flavor. You can find KORU apples at Market Basket if you’re in the Boston area like me.

Whole Wheat Morning Glory Muffins - Daisybeet

What’s in these morning glory muffins?

There are a fair amount of ingredients in this recipe, but don’t let that deter you from trying it! You can also make substitutions for several of the ingredients based on what you have on hand.

  • Whole wheat pastry flour: This flour is lower in gluten and ground into a finer texture than regular whole wheat flour, so it’s great for lighter baked goods like these muffins.
  • Carrots: These add lots of texture and chew to the muffins.
  • KORU apple: The bits of grated apple in these muffins are so delicious. If you can’t find KORU apples, I recommend using Fuji or Gala.
  • Brown sugar: You just need half a cup to make these perfectly sweet enough.
  • Applesauce: Applesauce is a wonderful replacement for oil in baked goods, especially these muffins, to let the apple flavors shine!
  • Flax meal: Ground flax adds a boost of fiber and plant-based omega-3 fatty acids to this recipe.
  • Orange zest: The orange zest puts the “morning” in morning glory! 
  • Maple syrup: Just 2 tablespoons to add a little delicious maple flavor.
  • Golden raisins: I used golden raisins because I had them on hand. Feel free to use regular raisins, dried cranberries, or another dried fruit in their place.
  • Walnuts: I love walnuts in muffins. Pecans would be a good substitute for walnuts in this recipe.
  • Cardamom: If you don’t have cardamom in your spice cabinet, ground ginger would taste great with these muffins instead. 
  • Cinnamon
  • Eggs
  • Almond milk
  • Baking powder
  • Salt
Whole Wheat Morning Glory Muffins - Daisybeet

Tips for making this recipe perfectly

  • Don’t use pre-grated carrots from the store. The “matchstick” carrots you can buy at the store are too thick for baked goods. Grate carrots yourself using a grater or food processor.
  • Set out all your ingredients before you make the batter. Since there are quite a few ingredients in this recipe, it helps to pull out all your ingredients so you can quickly and efficiently prepare the muffin mix.
  • Store in the refrigerator. Since these muffins have carrots and apples, it’s best to store them in the fridge to keep them fresh.
Whole Wheat Morning Glory Muffins - Daisybeet

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Whole Wheat Morning Glory Muffins

These healthy whole wheat morning glory muffins are such a treat to wake up to! They’re filled with good-for-you ingredients like shredded apples, carrots, and raisins.

  • Author: Alex
  • Prep Time: 20 minutes
  • Cook Time: 25 minutes
  • Total Time: 45 minutes
  • Yield: 15 muffins 1x
  • Category: breakfast


  • 2 cups whole wheat pastry flour
  • 1 tsp baking powder
  • ½ tsp Kosher salt
  • 2 tsp cinnamon
  • ½ tsp cardamom
  • 2 tbsp flax meal
  • ½ cup brown sugar
  • ½ cup almond milk
  • ⅔ cup unsweetened applesauce
  • 2 large eggs
  • 2 tbsp maple syrup
  • 2 cups grated carrots 
  • 1 KORU apple, grated
  • ½ cup golden raisins
  • ½ cup walnuts, roughly chopped


  1. Preheat oven to 375F. Line a muffin tin with paper liners.
  2. In a large bowl, mix together flour, baking powder, salt, cinnamon, cardamom, flax meal, and brown sugar.
  3. In another bowl, whisk together almond milk, applesauce, eggs, and maple syrup.
  4. Pour wet ingredients into dry and mix to combine.
  5. Stir in grated carrots, apple, raisins, and walnuts.
  6. Scoop batter into muffin liners, filling about ¾ full.
  7. Bake for 20-25 minutes, until a toothpick inserted comes out clean.
  8. Let muffins cool before removing.


Store in an airtight container in the fridge.

Keywords: morning glory muffins, whole wheat

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Whole Wheat Morning Glory Muffins  - Daisybeet

Thank you Yes! Apples for sponsoring this blog post! I’m grateful to partner with brands I love to cook with, and all opinions are my own.