
Looking for a delicious way to use up sourdough discard while sneaking in some extra protein? These chocolate chip protein mini muffins are the answer. Made with real sourdough starter and vanilla protein powder, they strike the perfect balance between a wholesome snack and an indulgent treat — no dry, chalky “protein muffin” texture here, just soft, moist, bakery-style muffins with pockets of melted chocolate chips in every bite.
This recipe is ideal for anyone searching for high protein muffin recipes, easy sourdough discard recipes, or healthy mini muffins for meal prep. Each muffin delivers a boost of protein alongside the tangy depth that only sourdough discard can bring, making them a smarter alternative to store-bought protein bars or sugary muffin mixes. They’re freezer-friendly, kid-approved, and perfect for meal-prepped breakfasts, post-workout snacks, school lunches, or a quick grab-and-go bite.
Whether you’re a sourdough baker with extra discard piling up in the fridge, or you’re simply after a protein-packed snack that doesn’t taste like one, this mini muffin recipe checks every box: quick to make, easy to customize, and impossible to stop at just one.
Sourdough Chocolate Chip Mini Muffins

Wet Ingredients
- 1 Cup (200 g) Granulated Sugar
- 1 stick Softened Butter
- 1/2 Cup (125g) Sourdough Discard
- 3/4 Cup (185g) Greek Yogurt
- 1/4 Cup (60g) Milk
- 2 Eggs
Dry Ingredients
- 2 Cups (240g) All Purpose Flour
- 1 ½ Cups Mini Chocolate Chips
- 2 Scoops Vanilla Isopure Protein
- 1 Tsp Salt
- ½ Tsp Baking Soda
Directions
- Preheat the oven to 350°
- In a large mixing bowl, whisk together the flour, protein, salt & baking soda
- In the bowl of a stand mixer combine the softened butter, eggs & granulated sugar and cream together
- Once creamed add in yogurt & milk
- Slowly add dry ingredient into wet only until just combined, do not overmix
- Using a spatula fold in mini chocolate chips until they are evenly distributed
- Use a small cookie scoop to scoop the dough into a greased mini muffin container -sprinkle a few extra chips on top if you would like extra chocolate
- Bake the muffins for 15-18 minutes until a toothpick comes out clean
- Remove the muffins from the oven and allow them to cool completely in the muffin tin
Nutrition Facts
Per mini muffin:
| Yield | Calories | Protein | Fat | Carbs |
|---|---|---|---|---|
| 36 muffins | ~124 kcal | ~3.5 g | ~4.9 g | ~17 g |
| 42 muffins (mid) | ~106 kcal | ~3.0 g | ~4.2 g | ~14 g |
| 48 muffins | ~93 kcal | ~2.6 g | ~3.7 g | ~13 g |
Sourdough discard: assumed a standard 100% hydration starter (roughly half flour, half water by weight)
Greek yogurt: assumed plain, 2% lowfat
Chocolate chips: assumed standard semisweet mini chips (like Nestlé Toll House)
Isopure Vanilla protein: assumed the Zero Carb formula (~110 cal, 25g protein, 0g carb per scoop) — if you’re using a different Isopure line (they have a few), the numbers shift a bit, mostly in carbs/fat
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