Sourdough Chocolate Chip Muffins

These sourdough chocolate chip muffins are soft, fluffy, and perfectly sweet with a subtle tang — just like my sourdough discard zucchini muffins.

Looking for a heartier breakfast muffin? Try my pumpkin spice latte breakfast muffins — I make those year-round, they're not just for fall!

Ingredients

• sourdough discard: The star — straight from the fridge at 100% hydration, adding moisture and a subtle tang.
• eggs + milk: Bind the batter and add structure.
• neutral oil (or melted butter): Keeps the crumb moist and tender for days.
• Greek yogurt (or sour cream): Adds richness and a soft, plush texture.
• vanilla + sugar: Sweeten and round out the flavor.
• all-purpose flour + leaveners + salt: The structure and a reliable, tall rise.
• chocolate chips: Folded through and pressed on top for melty chocolate in every bite.

See recipe card for quantities.

Easy Substitutions & Variations

• Milk: Use a high-fat non-dairy milk like full-fat oat milk to keep them dairy-free.
• Butter/oil: A neutral oil or a plant-based butter both work.
• Greek yogurt: Swap 1:1 with sour cream, or use a non-dairy yogurt.
• Cozy spice: Add 1 teaspoon cinnamon and ½ teaspoon each of nutmeg, cardamom, and ginger — the same warm blend I love in my sourdough malted chai chocolate chip cookies.
• Different flavor: Love this two-temperature muffin method? Try it with fruit in my lemon raspberry muffins.

How to Make Sourdough Chocolate Chip Muffins

Note: I bake by weight for accuracy. Cup measurements are approximate and may vary depending on how you scoop.

Step 1: Combine the wet ingredients: Preheat your oven to 425°F and line a 12-cup muffin pan, lightly greasing the top of the pan. In a bowl, whisk the sourdough discard, sour cream, oil, milk, eggs, and vanilla until smooth.

Step 2: Combine the dry ingredients: In a large bowl, whisk the flour, baking powder, baking soda, salt, and sugar.

Step 3: Make the batter: Pour the wet into the dry and fold gently with a spatula until just a few streaks of flour remain.

Step 4: Add the chocolate: Fold in the chocolate chips only until evenly distributed. The batter should be thick and scoopable, not pourable.

Step 5: Rest and fill: Let the batter rest 15 minutes. Divide between the cups, filling them very full (about 90–100g each, or two 3-tablespoon scoops). Top with a few extra chocolate chips and a sprinkle of coarse sugar.

Step 6: Bake: Bake at 425°F for 5 minutes, then — without opening the oven — lower to 350°F and bake 12–15 minutes more, until the tops are tall and golden and a toothpick comes out with a few moist crumbs. Cool 5 minutes in the pan, then transfer to a rack.

Weigh your ingredients! Using a kitchen scale ensures your measurements are accurate, which is key for getting consistent results in baking. It takes the guesswork out of measuring and helps your recipes turn out exactly as intended every time.

Expert Tips

1. Don't overmix the batter. Fold just until a few flour streaks remain — overmixing leads to sad, flat, tough muffins.
2. Rest the batter. A 15-minute rest hydrates the flour and helps the muffins bake up taller.
3. Fill the cups very full. About 90–100g of batter per cup is the secret to those big, bakery-style domes.
4. Trust the two-temperature bake. The hot start sets tall tops; the lower finish bakes them through. Keep the oven closed during the switch.
5. Cool before peeling liners. If using liners, wait until the muffins are cool to peel them, or they'll stick.

What Makes This Recipe Special?

The sourdough discard does double duty here — it uses up that jar in your fridge and adds a subtle tang that keeps these from tasting flatly sweet, the same depth that makes my sourdough cornbread muffins so good.

The other secret is the technique: a rested batter, very full cups, and a two-temperature bake for tall, domed, bakery-style tops. It's the kind of small-but-mighty detail that also elevates my sourdough discard funfetti layer cake. Serve them warm with coffee, or add a slice of chocolate chunk banana bread for a full breakfast spread.

Sourdough Chocolate Chip Muffins FAQs

Sourdough Chocolate Chip Muffins Troubleshooting Guide

Storage

• Store in an airtight container or bag at room temperature for 4–5 days (they keep for 7 but are best within 5).
• Freeze in a freezer-safe container with as much air removed as possible for up to 6 months.

Other Chocolate Chip Recipes to Consider

Sourdough Chocolate Chip Muffins

Audrey Grubb

These sourdough chocolate chip muffins are light, fluffy, and perfectly sweet with a slight sourdough tang.

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Prep Time 10 minutes mins

Cook Time 15 minutes mins

Total Time 25 minutes mins

Course Breakfast, Dessert

Cuisine American

Servings 12 Muffins

Calories 318 kcal

Equipment

• ▢
  Medium mixing bowl
• ▢
  Whisk
• ▢
  Mixing spoon or spatula
• ▢
  Muffin scoop (optional)
• ▢
  12-muffin pan
• ▢
  Muffin liners (optional)

Ingredients

  

1x2x3x

• ▢ 300 g all-purpose flour
• ▢ 12 g baking powder 3 teaspoons
• ▢ ½ teaspoon baking soda
• ▢ ¾ teaspoon fine salt
• ▢ 150 g granulated sugar
• ▢ 200 g sourdough discard 100% hydration
• ▢ 120 g sour cream room temperature
• ▢ 85 g neutral oil
• ▢ 90 g whole milk room temperature
• ▢ 2 large eggs room temperature
• ▢ 2 teaspoons vanilla extract
• ▢ 180 g semi-sweet chocolate chips plus extra for the tops
• ▢ Coarse sugar optional, for topping

Instructions

 

• Prep the pan and oven. Preheat the oven to 425°F. Line a 12-cup muffin pan with liners and lightly grease the top of the pan to help prevent oversized muffin tops from sticking.
• Combine the dry ingredients. In a large bowl, whisk together the flour, baking powder, baking soda, salt, and sugar.
  300 g all-purpose flour, 12 g baking powder, ½ teaspoon baking soda, ¾ teaspoon fine salt, 150 g granulated sugar
• Combine the wet ingredients. In a separate bowl, whisk the sourdough discard, sour cream, oil, milk, eggs, and vanilla until smooth.
  200 g sourdough discard, 120 g sour cream, 85 g neutral oil, 90 g whole milk, 2 large eggs, 2 teaspoons vanilla extract
• Make the batter. Pour the wet ingredients into the dry ingredients. Fold gently with a spatula just until a few streaks of flour remain. Add the chocolate chips and fold only until evenly distributed. The batter should be thick and scoopable, not pourable.
  180 g semi-sweet chocolate chips
• Rest and fill. Let the batter rest for 15 minutes. Divide it between the muffin cups, filling them very full, about 90–100 g batter per cup or roughly two 3-tablespoon scoops. Add a few extra chocolate chips and a sprinkle of coarse sugar to each top.
  Coarse sugar
• Bake. Bake at 425°F for 5 minutes. Without opening the oven, lower the temperature to 350°F and bake for another 12–15 minutes, until the tops are tall and golden and a toothpick inserted into the center comes out with a few moist crumbs.
• Cool. Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack.

Notes

For the best appearance, use regular-sized chocolate chips inside and press a few mini chips or chopped chocolate pieces onto the tops before baking.

Nutrition

Calories: 318kcalCarbohydrates: 45gProtein: 5gFat: 14gSaturated Fat: 5gPolyunsaturated Fat: 4gMonounsaturated Fat: 2gTrans Fat: 0.04gCholesterol: 28mgSodium: 228mgPotassium: 114mgFiber: 1gSugar: 22gVitamin A: 51IUCalcium: 76mgIron: 1mg

Tried this recipe?Let us know how it was!

Food safety

• Wash hands after touching raw egg or flour.
• Never leave a hot oven unattended.
• Always have good ventilation when using a gas stove

See more guidelines at USDA.gov.