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Close-up of a sourdough morning glory muffin highlighting the textured surface with visible raisins and grated carrot throughout.

Healthy Sourdough Morning Glory Muffins With Fresh Milled Wheat

These healthy sourdough morning glory muffins are made with fresh milled wheat, grated fruits and vegetables, and sourdough starter for a nourishing from-scratch bake. Lightly sweetened and full of texture, they are a wholesome muffin perfect for breakfast or a simple snack.
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Course: Breakfast
Cuisine: American
Prep Time: 15 minutes
Cook Time: 18 minutes
Total Time: 33 minutes
Servings: 12 muffins
Author: Stephanie

Equipment

  • Muffin pan
  • Paper liners or grease for the pan
  • Large mixing bowl
  • Medium mixing bowl
  • Box grater
  • Whisk
  • Rubber spatula or wooden spoon

Ingredients

Dry Ingredients

  • 2 cups soft milled wheat flour 286 g
  • 1 tablespoon additional soft milled wheat flour 14 g
  • 2 teaspoons baking powder
  • ½ teaspoon baking soda
  • 1 tablespoon ground cinnamon
  • ½ teaspoon ground ginger
  • ½ teaspoon salt

Add-Ins

  • 1 large apple peeled, cored, and finely grated
  • 1 large carrot peeled and finely grated (1 cup)
  • ½ cup raisins
  • Zest of 1 orange
  • 2 tablespoons fresh orange juice
  • ½ cup chopped pecans

Wet Ingredients

  • ½ cup sourdough starter discard 125 g
  • ⅔ cup sucanat sugar or ½ cup raw honey (reduce greek yogurt by 2 tablespoons)
  • 5 tablespoons butter 70 g, melted and cooled
  • 2 large eggs
  • 3 tablespoons whole-milk Greek yogurt or sour cream 45 g
  • 1 teaspoon vanilla extract

Instructions

  • Preheat your oven to 350°F and line a muffin tin with paper liners or lightly grease each cup. In a large bowl, whisk together the soft milled wheat flour, additional flour, baking powder, baking soda, cinnamon, ginger, and salt.
  • Stir in the grated apple, grated carrot, raisins, orange zest, orange juice, and chopped pecans until evenly distributed.
  • In a separate bowl, whisk together the sourdough discard, sucanat sugar or honey, melted butter, eggs, yogurt or sour cream, and vanilla extract.
  • Pour the wet ingredients into the dry ingredients and gently fold until just combined. Do not overmix.
  • Divide the batter evenly among the muffin cups, filling each about three-quarters full.
  • Bake for 18 to 22 minutes, or until the tops are set and a toothpick inserted in the center comes out clean. Let the muffins cool in the pan for 5 minutes before transferring to a wire rack to cool completely.

Notes

Overnight Fermentation Option

For an overnight sourdough breakfast, mix the wet ingredients and fresh milled wheat flour the night before, cover, and let the batter rest at room temperature for 8–12 hours. In the morning, gently fold in the baking powder, baking soda, salt, and remaining add-ins just before baking. This slow rest helps the flour fully hydrate, softens the bran, and develops a deeper flavor while keeping the muffins tender and hearty.

Tips for Healthy Sourdough Morning Glory Muffins

  • Use freshly milled wheat right away for the best texture and flavor. Fresh flour absorbs moisture quickly, so mix the batter as soon as the grain is milled.
  • Squeeze excess moisture from grated carrots or apples to prevent dense or soggy muffins.
  • Do not overmix the batter. Stir just until combined to keep the muffins tender.
  • Let the batter rest for 10 to 15 minutes before baking to allow the fresh milled wheat to fully hydrate.
  • Check for doneness early. Fresh milled wheat muffins can bake faster, so test with a toothpick a few minutes before the timer ends.