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sourdough apple muffins in a basket

How to Make the Best Sourdough Apple Muffins – With Pecan Crumble!


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  • Author: MJD
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x

Description

Soft, fluffy, and packed with warm cinnamon and juicy apples, these sourdough apple muffins are made with 100% whole grains and topped with a buttery pecan crumble. Using sourdough discard keeps them extra moist with a subtle tang, making them a wholesome and delicious breakfast or snack. Perfect for meal prep, they freeze beautifully and reheat in seconds!


Ingredients

Scale

Muffins:

  • 78g Spelt Flour (or substitute with all purpose flour)
  • 78g Whole Wheat Flour
  • 2g Ground Cinnamon (½ tsp)
  • 4g Baking Powder (1 tsp)
  • 4g Baking Soda (¾ tsp)
  • 3g Kosher Salt (½ tsp)
  • 94g Butter, melted (⅓ cup)
  • 115g Maple Syrup (⅓ cup)
  • 128g Apple, peeled & chopped (about 1 cup)
  • 41g Egg, room temperature (1 large)
  • 3g Vanilla Extract (¾ tsp)
  • 81g Sourdough Discard (about ⅓ cup)
  • 234g Greek Yogurt (1 cup)

Pecan Crumble Topping:

  • 50g Chopped Pecans (½ cup)
  • 30g Whole Wheat Flour (¼ cup)
  • 12g Rolled Oats (2 tbsp)
  • 24g Brown Sugar (2 tbsp)
  • 1.5g Cinnamon (½ tsp)
  • 1g Salt (¼ tsp)
  • 28g Butter, melted (2 tbsp)
  • 21g Honey (1 tbsp)

Instructions

Prepping the Ingredients:

  1. Chop the apples finely for even distribution in the batter.
  2. Mix the wet and dry ingredients separately to prevent overmixing.

Making the Batter:

  1. In a small bowl, whisk together flour, baking powder, baking soda, cinnamon, and salt. Set aside.
  2. In a large bowl, whisk together melted butter and maple syrup.
  3. Add vanilla extract, Greek yogurt, and egg, whisking until smooth.
  4. Stir in sourdough discard until fully combined.
  5. Gently fold the dry ingredients into the wet until just combined—do not overmix.
  6. Fold in chopped apples, distributing evenly.

Pecan Crumble Topping:

  1. In a small bowl, mix pecans, flour, oats, brown sugar, cinnamon, and salt.
  2. Stir in melted butter and honey until crumbly.
  3. Sprinkle over muffins, gently pressing into the batter.

Baking:

  1. Preheat oven to 425°F (218°C). Line a muffin tin with liners.
  2. Divide batter evenly into muffin cups, filling ¾ full.
  3. Bake at 425°F (218°C) for 5 minutes, then reduce heat to 375°F (190°C) and bake for another 15-18 minutes, until a toothpick inserted in the center comes out clean.
  4. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack.

Notes

  • For extra crunch: Stir some chopped pecans into the batter.
  • For a nut-free version: Swap pecans for sunflower or pumpkin seeds.
  • For best texture: Avoid overmixing—the batter should be just combined.
  • To freeze: Store in an airtight container for up to 2 months. Reheat in the microwave for 20-30 seconds or warm in a 300°F (150°C) oven for 5-10 minutes.
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Category: Breakfast, Snack
  • Method: Baking
  • Cuisine: Sourdough, Whole Grain