Sprouted Flour Sourdough Muffins – Healthy, Overnight Recipe

There’s nothing cozier than the smell of apple cinnamon muffins baking in the oven. These healthy sourdough apple muffins with collagen are a nourishing twist on a classic, made with sprouted flour, sourdough starter, and naturally sweetened with coconut sugar and applesauce.

The added collagen peptides blend right in, giving the muffins a protein boost—making them more satisfying for breakfast, snacks, or lunchboxes. Perfect for families, kids, and anyone looking for a wholesome fall treat.

Whether you’re looking for a way to use up sourdough discard or want a more blood sugar–friendly muffin, this recipe is one you’ll want to make again and again.

Why These Muffins Are Different

Sprouted flour – Sprouting makes grains easier to digest, unlocks more available nutrients (like B vitamins and minerals), and can reduce their impact on blood sugar compared to regular flour.

Sourdough starter – The natural fermentation process helps break down gluten and phytic acid, supporting digestion and nutrient absorption. Fermented grains also tend to have a gentler effect on blood sugar.

Collagen peptides – Adds extra protein without changing the flavor or texture, supporting satiety, skin, and joint health.

Kid-friendly – Soft, lightly sweetened, and toddler-approved. Pair with a protein (like nut butter, cheese, or eggs) for balanced energy and steady blood sugars.

Sourdough Apple Muffin Recipe with Collagen

Ingredients (makes 12 muffins):

• 1 cup (240 g) sourdough starter (active or discard)
• 1 ½ cups (180 g) sprouted soft white wheat flour
• 4 Tbsp (32 g) collagen peptides (unflavored) – optional but encouraged for protein boost
• 1 tsp (5 g) baking soda
• 1 tsp (4 g) baking powder
• ½ tsp (3 g) salt
• 2 tsp (5 g) ground cinnamon
• ½ cup (113 g) unsalted butter, melted
• ½ cup (120 g) unsweetened applesauce
• ⅓ cup (45 g) coconut sugar (or date sugar)
• 2 large eggs (about 100 g total) – pasture raised preferred
• 1 tsp (5 ml) vanilla extract
• 1 medium apple, peeled and finely chopped (about 120 g)

Instructions

Same-Day Baking:

1. Preheat oven to 350°F (175°C) and line a muffin tin with paper liners.
2. In a large mixing bowl, whisk together sourdough starter, melted butter, applesauce, coconut sugar, eggs, and vanilla.
3. In another bowl, stir together flour, collagen peptides, baking soda, baking powder, salt, and cinnamon.
4. Gently fold dry ingredients into wet until just combined. Stir in chopped apple.
5. Divide batter evenly into 12 muffin cups.
6. Bake 18–22 minutes, until a toothpick inserted in the center comes out clean.
7. Cool slightly and enjoy warm.

Overnight Fermentation Option (for easier digestion & deeper flavor):

1. The night before, mix everything except the baking soda and baking powder. Cover the bowl tightly and refrigerate overnight.
2. In the morning, preheat oven to 350°F (175°C). Stir the baking soda and baking powder into the chilled batter until well combined.
3. Portion into muffin cups and bake as directed (18–22 minutes).

Tips for Success

• Make Ahead: These muffins keep well in an airtight container at room temperature for 2–3 days, or freeze up to 2 months.
• Blood Sugar Balance: While these muffins are more nutrient-dense and lower glycemic than conventional recipes, pairing them with protein or healthy fats (like eggs, nut butter, or yogurt) is the best way to support steady blood sugar.
• Sweetness: This recipe is lightly sweetened. If you prefer sweeter muffins, add an extra tablespoon of coconut sugar or drizzle with honey after baking.

Frequently Asked Questions

Can I use sourdough discard for these muffins?

Yes! This recipe works with both active starter and discard.

Can I substitute regular flour?

You can use all-purpose flour if you don’t have sprouted flour, though you’ll lose some of the nutrient-dense and blood sugar–friendly benefits.

Do kids like these?

Absolutely. They’re moist, soft, and not overly sweet—perfect for toddlers and older kids.

These sourdough apple cinnamon muffins with collagen are a cozy, nutrient-dense option that’s family-friendly and functional. If you give them a try, share a photo and tag me—I’d love to see how they turn out in your kitchen!

Download the PDF of this recipe and print it for yourself!

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