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

Soft, fluffy, and packed with warm cinnamon and juicy apples, these sourdough apple muffins are a go-to in our house—my kids absolutely LOVE them! Made with 100% whole grains and a buttery pecan crumble topping, they’re the perfect wholesome breakfast or snack. Plus, they use sourdough discard, keeping them moist with a subtle tang while reducing waste. If you love easy sourdough baking, this is a must-try!

Why You’ll Love These Muffins

These healthy apple muffins with sourdough are light, fluffy, and packed with warm cinnamon flavour. The addition of sourdough discard not only reduces waste but also adds moisture and a subtle tang that balances the sweetness. Made with 100% whole grains, they’re hearty, nutritious, and perfect for meal prep.

• Uses sourdough discard – A great way to use up extra discard while adding flavor and tenderness. Learn how to maintain your sourdough starter here.
• Packed with apple flavour – Fresh apple chunks give these muffins a naturally sweet, juicy bite in every bite.
• 100% whole grain – Made with whole wheat flour or fresh-milled flour for better nutrition and depth of flavour.
• Crunchy pecan crumble – A buttery, slightly sweet topping adds the perfect texture, but you can omit it for a sugar-free version.
• Perfect for busy mornings – These muffins freeze well and reheat easily, making them great for breakfast, snacks, or kids’ lunches.

Ingredients & Substitutions for Sourdough Apple Muffins

These muffins are made with 100% whole grains, combining whole wheat and spelt flour for a hearty texture and rich flavor. The addition of sourdough discard keeps them moist and tender, while fresh apples add natural sweetness. A hint of cinnamon brings warmth, and the buttery pecan crumble on top adds the perfect crunch.

Pecan Crumble Topping Ingredients

Ingredient Breakdown & Functions

• Sourdough Discard – Adds moisture, a mild tang, and helps create a soft, tender crumb. Using discard also reduces waste.
• Whole Wheat & Spelt Flour – These whole grains add fibre, nutrition, and a slightly nutty flavour. For the best taste and nutritional value, try using fresh-milled flour. Learn how to mill your own flour here.
• Apples – Provide natural sweetness and moisture. Honeycrisp and Granny Smith are great options for a balance of tartness and sweetness.
• Pecan Crumble Topping – A buttery, crunchy topping that adds texture and flavor. It can be omitted for a sugar-free version.
• Cinnamon & Spices – Enhance the warm, cozy flavor that pairs perfectly with apples.
• Butter or Oil – Butter adds richness and flavor, while oil keeps the muffins extra moist. Choose based on your preference.
• Maple Syrup or Honey – Natural sweeteners that complement the apples and add depth to the flavour.

Sourdough Apple Muffins Customization Options

• Flour Alternatives – This recipe is designed for whole grains, but you could try a cup-for-cup gluten-free flour blend if needed. Results may vary.
• Dairy-Free – Swap butter for coconut oil or a neutral vegetable oil to keep the muffins moist.
• Fruit Swap – You can replace apples with diced pears for a slightly different but equally delicious flavour.
• Extra Crunch? – Stir chopped pecans into the batter for added texture.

Equipment Needed

• Mixing Bowls – One for wet ingredients, one for dry.
• Whisk – For smoothly combining wet ingredients.
• Spatula – Helps fold the batter gently without overmixing.
• Muffin Tin – Standard 12-cup tin for even baking.
• Muffin Liners – Prevents sticking and makes cleanup easy.
• Kitchen Scale – For precise ingredient measurements.
• Measuring Cups & Spoons – If not using a scale.
• Wire Rack – Helps sourdough apple muffins cool properly to avoid sogginess.

Step-by-Step Instructions

Prepping the Ingredients

• Chop the apples finely – Smaller pieces ensure even distribution and prevent them from sinking in the batter.
• Mix the wet and dry ingredients separately – This prevents overmixing and helps create a light, fluffy texture.

Making the Batter (The Secret to Fluffy Muffins!)

1. Prepare the dry ingredients – In a small bowl, whisk together the whole wheat flour, spelt flour, baking powder, baking soda, cinnamon, and salt. Set aside.
2. Mix the wet ingredients – In a large bowl, whisk together the melted butter and maple syrup until well combined.
3. Incorporate the remaining wet ingredients – Add the vanilla extract, Greek yogurt, and egg, whisking until smooth.
4. Add the sourdough discard – Stir until fully combined.
5. Gently fold in the dry ingredients – Mix just until combined to avoid overworking the batter.
6. Fold in the apples – This should be the last step before portioning out the batter.

Note:

• Don’t Overmix! Why Gentle Folding Matters – Overmixing develops too much gluten, making the muffins dense instead of light and fluffy. Fold the ingredients just until combined—a few streaks of flour are okay!

Pecan Crumble Topping

1. Make the streusel – In a small bowl, combine chopped pecans, whole wheat flour, rolled oats, brown sugar, cinnamon, and salt.
2. Add melted butter and honey – Mix with a fork until crumbly.
3. Sprinkle over muffins – Lightly press it into the batter before baking.

Notes:

• Using cold butter or chilling the topping before baking creates better crumbles and helps achieve that bakery-style crunch.
• For extra crispiness, bake the muffins at a slightly higher temperature for the first few minutes before lowering the heat.

Baking Tips for Success

1. Start at high heat, then lower for a perfect rise – Bake at 425°F (218°C) for the first 5 minutes, then reduce to 375°F (190°C) for the remaining time. This helps create tall, domed muffins.
2. How to test for doneness – Insert a toothpick or knife into the center—if it comes out clean or with just a few crumbs, the muffins are ready.
3. Cooling properly – Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to prevent fogginess.
4. These whole grain sourdough muffins bake up perfectly golden with a soft interior, thanks to the balance of sourdough discard and Greek yogurt keeping them moist.

Pro Tips for the Best Sourdough Apple Muffins

Making the perfect sourdough apple muffins comes down to a few key techniques. These simple tips will help you achieve a light, fluffy texture, balanced flavour, and the perfect rise.

Use Room Temperature Ingredients

Cold ingredients can prevent the batter from mixing properly, leading to dense muffins. Let your eggs, milk, and sourdough discard come to room temperature before baking to ensure even incorporation and a better rise.

Coat Apples in Flour to Prevent Sinking

To keep the apple pieces evenly distributed, toss them in a small amount of flour before folding them into the batter.

Why Sourdough Discard Makes Muffins Extra Moist

Sourdough discard not only adds a slight tangy depth to these muffins, but it also helps retain moisture. Thanks to the natural fermentation process, discard creates a softer crumb and keeps the muffins from drying out too quickly.

Achieve the Perfect Muffin Rise

Start baking at a higher temperature (like 425°F/218°C) for the first 5 minutes, then lower the heat for the remainder of the bake. This encourages a rapid rise, giving your muffins a tall, domed top instead of spreading flat.

Don’t Overmix the Batter

Overmixing develops too much gluten, leading to tough muffins. For the best texture, gently fold the wet and dry ingredients together just until combined—a few streaks of flour are fine.

Get a Golden, Crunchy Crumble Topping

For a crisp, bakery-style crumble, make sure the butter in your pecan topping is cold when mixing. This helps create small clumps that crisp up beautifully in the oven. If you want extra crunch, sprinkle a few more chopped pecans on top before baking.

Storage & Freezing Instructions

Healthy muffins are something we always have on hand, and we rotate through different recipes depending on the season. These sourdough apple muffins are a favourite, and we love to freeze them for an easy, grab-and-go breakfast or snack for the kids. A quick reheat in the microwave makes them soft and warm, perfect for busy mornings.

Storing at Room Temperature

For short-term storage, place the muffins in an airtight container at room temperature. We usually only keep out what we’ll eat within two days, as we prefer to freeze the rest to keep them fresh.

Freezing for Long-Term Storage

To keep muffins fresh for longer, store them in a sealed container or freezer bag for up to two months. Freezing them individually or in small batches makes it easy to take out just what you need.

• Mini muffins freeze especially well! We often make a batch of minis because the kids love them, and they make a perfect quick fibre-filled snack.

Reheating for the Best Texture

• Microwave: The easiest way to reheat a frozen muffin is in the microwave—just heat for 20-30 seconds until warm and soft.
• Oven: If you have more time, warm them in the oven at 300°F (150°C) for 5-10 minutes to restore their freshly baked texture.

FAQs About Sourdough Apple Muffins

Can I use active sourdough starter instead of discard?

Yes! You can use an active sourdough starter to make sourdough apple muffins, but since it contains more hydration, you may need to reduce the other liquids slightly to maintain the right batter consistency.

Can I make these without sourdough discard?

This recipe is designed to use sourdough discard, which adds moisture and flavour. If you don’t have any, you could try replacing it with equal parts yogurt or buttermilk for a similar texture, though the flavour will be slightly different.

Why did my muffins turn out dense?

Dense muffins are usually caused by overmixing the batter or using too much flour. To keep them light and fluffy, mix gently just until combined and be sure to measure your flour correctly using a scale or the spoon-and-level method.

Can I swap pecans for another nut?

Absolutely! Walnuts or almonds work well as a substitute in the crumble topping or mixed into the batter. If you prefer a nut-free version, you can leave them out entirely or swap in pumpkin or sunflower seeds for a bit of crunch.

If you love baking with sourdough discard, here are more delicious recipes to reduce waste while making something amazing. Try these next!

• Sourdough Discard Tortillas – Soft and flexible, perfect for wraps and tacos.
• Sourdough Discard Crackers – Crispy, savoury, and packed with sourdough flavour.
• Sourdough English Muffins – Nooks, crannies, and the perfect chew.
• Sourdough Discard Biscuits – Flaky, buttery, and incredibly easy to make.

Final Thoughts – Share Your Results!

I’d love to hear how these sourdough apple muffins turned out for you! If you make them, leave a comment and rating below—your feedback helps others and supports my site.

Want more sourdough baking tips and recipes? Join my newsletter here to get expert advice straight to your inbox!

Looking for step-by-step tutorials? Check out my YouTube channel for in-depth sourdough guides and techniques.

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

---

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 1 review

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

Print Recipe

Pin Recipe

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 1x2x3x

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)

Cook Mode Prevent your screen from going dark

---

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:

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

Pecan Crumble Topping:

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

Baking:

12. Preheat oven to 425°F (218°C). Line a muffin tin with liners.
13. Divide batter evenly into muffin cups, filling ¾ full.
14. 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.
15. 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