Baked Sourdough Discard Mac & Cheese

This baked sourdough discard mac and cheese is the best way to turn extra starter into something rich, cozy, and satisfying. This isn’t just another mac and cheese recipe. It’s true farmhouse comfort.

The sourdough discard adds a gentle tang that balances the creamy, cheesy sauce. You won’t get that flavor from a boxed mix or even a regular homemade version. Topped with buttery breadcrumbs and baked until golden and bubbling, it’s the kind of dish that feels special for Sunday dinner but simple enough for a weeknight.

If you’re already on a sourdough journey, don’t miss my sourdough discard sandwich bread or these easy sourdough discard waffles for more ways to make every scoop of discard count. And if you don’t have any sourdough, you might want to try my easy cast iron skillet mac and cheese.

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A serving of baked sourdough discard mac and cheese on a white plate topped with buttery breadcrumbs, next to a baking dish on a green checkered cloth.

Why You’ll Love This Recipe

  • Uses up sourdough discard: A practical and delicious way to avoid waste in your kitchen.
  • Made with simple ingredients: No fancy cheeses or hard-to-find items, just pantry staples from a typical farmhouse kitchen.
  • Farmhouse flavor: The sourdough adds a subtle tang that deepens the flavor of the cheese sauce.
  • Kid-approved comfort food: Creamy, cheesy, and cozy…Perfect for weeknight dinners or a side dish.
  • Quick to make: This sourdough mac & cheese recipe comes together in under 30 minutes with minimal prep and cleanup.
  • Easy to customize: Add vegetables, swap cheeses, or top with crispy breadcrumbs for a baked version.
Baked sourdough discard mac and cheese topped with golden, crunchy breadcrumbs and garnished with fresh herbs.

Ingredients

  • Sourdough discard: either fed or unfed, doesn’t matter in this recipe!
  • Breadcrumbs: for the crunchy topping
  • Butter: melted, and unsalted
  • Flour: all purpose flour
  • Milk: whole milk, or 2% works in a pinch!
  • Cheese: parmesan and sharp cheddar cheese
  • Dijon mustard: Optional but adds depth
  • Salt and pepper: to taste
Baked sourdough discard mac and cheese topped with golden breadcrumbs, served in a white casserole dish on a green checkered cloth.

Recipe Tips

Use room temperature discard: Cold discard can cause the sauce to separate or clump. Let it sit out for 15–20 minutes before using.

Whisk constantly when making the roux: This prevents lumps and ensures a smooth, creamy base.

Shred your own cheese: Pre-shredded cheese contains anti-caking agents that can make the sauce grainy.

Don’t boil the sauce after adding cheese: Keep the heat low to avoid curdling.

Adjust thickness as needed: If the sauce is too thick, add a splash of milk; if too thin, let it simmer a little longer.

Taste before serving: Sourdough discard varies in tanginess, add a pinch more salt or cheese if needed.

Make it ahead: You can make the sauce in advance and store it in the fridge for up to 2 days, just reheat gently before mixing with pasta.

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A serving of baked sourdough discard mac and cheese topped with golden breadcrumbs on a white plate next to a grey and green checkered cloth.

New to baking with discard? Be sure to check out my beginner’s sourdough discard bread for another easy loaf that doesn’t require a stand mixer.

Instructions

  1. Cook the pasta: Bring a large pot of salted water to a boil. Add your elbow macaroni and cook just until al dente—tender but still with a little bite. Drain the noodles and set them aside while you prepare the cheese sauce.
  2. Make the roux: In a medium saucepan over medium heat, melt the butter. Once it’s fully melted and gently bubbling, sprinkle in the flour. Whisk it constantly for about 1–2 minutes to cook out the raw flour taste. The mixture should be smooth and lightly golden, like a creamy paste.
  3. Stir in milk and sourdough discard: Slowly pour in the milk while whisking to keep everything smooth. Then whisk in your sourdough discard. Keep stirring as the mixture gently heats and thickens (this takes about 5 minutes). You’ll know it’s ready when it coats the back of a spoon.
  4. Add the cheese and seasoning: Turn the heat to low and stir in the shredded cheddar, grated parmesan, Dijon mustard (if using), salt, and black pepper. Stir gently until the cheese is completely melted and the sauce is velvety smooth.
  5. Combine pasta and sauce: Pour the cooked pasta into the cheese sauce and stir until every noodle is coated with that creamy, tangy goodness. You can do this in the saucepan or right in your baking dish if it’s large enough.
  6. Transfer to baking dish: Lightly butter a 9×13” casserole dish and spoon in your mac and cheese. Spread it out evenly with the back of a wooden spoon.
  7. Make the breadcrumb topping: In a small bowl, mix the breadcrumbs with melted butter. If you’re using parmesan or a sprinkle of herbs, add them now. Stir until the crumbs are evenly moistened.
  8. Top and bake: Sprinkle the buttery breadcrumbs evenly over the top of the mac and cheese. Pop the dish into a preheated 375°F oven and bake uncovered for 15–20 minutes, or until the top is golden brown and bubbling around the edges.
  9. Cool slightly and serve: Let the dish rest for about 5–10 minutes before serving. It helps the sauce settle a bit and makes each scoop easier to serve—and even more satisfying.

FAQ

Yes! Fed, bubbly starter will work just fine in this recipe. It might be slightly milder in tang, but it still adds great flavor and creaminess to the sauce.

Sharp cheddar is classic and adds a rich, farmhouse flavor, but you can mix in mozzarella for stretchiness, gouda for creaminess, or pepper jack for a little heat. Just make sure you shred it yourself for the best melt.

Yes—just use your favorite gluten-free pasta and swap the flour in the roux for a gluten-free blend or even cornstarch. You may need to adjust the amount slightly for thickening.

Add in chopped cooked bacon, shredded chicken, or even roasted veggies like broccoli or cauliflower. It’s a great base for turning leftovers into something cozy and new.

Keep leftovers in an airtight container in the fridge for up to 3 days. Reheat in a saucepan over low heat with a splash of milk to bring back that creamy texture.

Mac and cheese can be frozen, but the texture may change slightly. Freeze in a tightly sealed container and reheat gently with a bit of milk to revive the sauce.

I like to batch bake and freeze my homemade staples. My Simple Kitchen Printable Bundle helps me stay organized when cooking from scratch.

Recipe Variations & Substitutions

  • Veggie packed: Stir in steamed broccoli, peas, spinach, or roasted cauliflower for a nourishing boost.
  • Farmhouse three cheese: Use a mix of sharp cheddar, mozzarella, and gouda for a richer, creamier flavor.
  • Smoky & savory: Add chopped bacon or ham and a pinch of smoked paprika or chipotle powder for depth.
  • Gluten-free friendly: Use gluten-free elbow pasta and swap the flour in the roux for a gluten-free blend or cornstarch.
  • Breadcrumbs: If you’d rather skip the breadcrumbs, try topping your mac and cheese with a layer of parmesan or sharp cheddar for a golden, cheesy crust.
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5 from 1 vote

Baked Sourdough Discard Mac & Cheese

This sourdough discard mac and cheese is rich, creamy, and packed with farmhouse flavor. A cozy way to use up your sourdough starter, whether served as a quick stovetop dinner or baked with buttery breadcrumbs for a Sunday side.
Prep Time:15 minutes
Cook Time:30 minutes
Total Time:45 minutes
Course: Dinner
Cuisine: American
Keyword: homemade mac and cheese recipe, sourdough, sourdough discard

Equipment

  • large pot To boil the pasta
  • Medium saucepan For the cheese sauce
  • Whisk To mix roux and prevent lumps
  • Wooden Spoon For stirring cheese and pasta
  • Box grater For freshly shredded cheese
  • Measuring Cups and Spoons For accurate ingredients
  • Casserole dish (9×13”): For baking
  • Small Bowl For mixing breadcrumbs

Ingredients

Mac & Cheese

  • 2 cups elbow macaroni
  • 3 tbsp butter
  • 3 tbsp all-purpose flour
  • 2 cups whole milk
  • ½ cup sourdough discard
  • 2 cups shredded sharp cheddar cheese
  • ½ cup freshly grated parmesan cheese
  • 1 tsp Dijon mustard optional
  • ½ tsp salt
  • ¼ tsp black pepper

Breadcrumb Topping

  • ¾ cup breadcrumbs
  • 2 tbsp butter melted
  • 2 tbsp grated parmesan optional

Instructions

  1. Cook the pasta: Bring a large pot of salted water to a boil. Add macaroni and cook just until al dente. Drain and set aside.
  2. Make the roux: In a medium saucepan over medium heat, melt the butter. Once melted, whisk in the flour and cook for 1–2 minutes until smooth and golden.
  3. Add milk and discard: Slowly whisk in the milk and sourdough discard until the mixture is smooth. Simmer over medium heat, whisking frequently, until thickened—about 5 minutes.
  4. Add cheese and seasonings: Turn the heat to low. Stir in the cheddar, parmesan, Dijon (if using), salt, and pepper. Mix until melted and creamy.
  5. Combine: Stir the cooked macaroni into the sauce until fully coated. Serve as-is or continue with baked version.
  6. Bake: Preheat oven to 375°F. Transfer mac and cheese to a buttered 9×13” baking dish. Mix breadcrumbs with melted butter and parmesan (if using), then sprinkle over the top. Bake uncovered for 15–20 minutes or until golden and bubbly. Let cool slightly before serving.

Notes

  • Use room temperature discard for easier blending into the sauce.
  • Shred your own cheese for the smoothest melt—pre-shredded often contains anti-caking agents.
  • Don’t boil the sauce after adding cheese to prevent it from separating.
  • Make it ahead: the sauce can be prepped and stored for 1–2 days in the fridge.

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