As I rummaged through my pantry, a forgotten jar of sourdough discard caught my eye, sparking a wave of inspiration. This was the perfect moment to whip up Healthy Sourdough Discard Kolaches with Cream Cheese Filling, a delightful treat that turns leftover starter into something extraordinary. Not only are these kolaches packed with the richness of ancient grains like einkorn and spelt, but they also promise a delightful contrast of textures—soft and tender dough enveloping creamy filling. They’re quick to prepare and make for a delicious breakfast or brunch option that the whole family will adore. Best of all, this recipe helps minimize food waste while indulging in a cherished Czech pastry tradition. Curious about how to bring these little delights into your kitchen? Let’s dive into the details!

Why Try Healthy Sourdough Discard Kolaches?
Versatile Treat: These kolaches can easily transition from breakfast to dessert, making them ideal for any occasion.
Unique Ingredients: The blend of einkorn and spelt flour gives a unique flavor profile that elevates your traditional pastry game.
Guilt-Free Indulgence: With their healthy twist, you can enjoy these delightful sweets without the worry of extra calories.
Waste Not, Want Not: Using sourdough discard not only reduces waste but also contributes to a deliciously tangy dough that you’ll crave.
Crowd-Pleaser: Warm, creamy, and soft, these kolaches are sure to impress family and friends, perfect for brunch gatherings!
If you love a good pastry as much as I do, check out my Healthy Protein Crepes or treat yourself with Pumpkin Protein Balls for a nutritious twist on your favorite snacks!
Healthy Sourdough Discard Kolaches Ingredients
For the Dough
- Einkorn flour – Provides a depth of flavor that enhances the overall taste.
- Spelt flour – Adds a nutty sweetness; if needed, you can swap it with whole wheat flour.
- Sourdough starter – Essential for that tangy flavor and vital for achieving the right rise in your kolaches.
- Milk – Use whole milk for added moisture and richness in your dough.
- Butter – Must be melted for proper incorporation into the dough.
- Sugar – Adjust the sweetness according to your taste; it sweetens both the dough and the filling.
- Egg + egg yolk – Provide necessary structure and richness; substitutions are not recommended.
- Salt – Enhances the flavor in both the dough and filling.
For the Cream Cheese Filling
- Cream cheese – The star of the filling; ensure it’s softened to create a smooth texture.
- Lemon juice – Brightens the flavor blend in the filling; adjust to personal preference.
For the Streusel Topping
- Flour – Typically all-purpose; forms a delightful crumbly layer on top of your kolaches.
- Butter (for streusel) – Mix with flour and sugar until sandy to achieve the desired texture.
- Sugar (for streusel) – Just the right amount adds sweetness to the topping.
These Healthy Sourdough Discard Kolaches not only offer a delicious way to use up leftover starter, but they also shine with the richness of ancient grains. Are you ready to bake a batch and indulge in a guilt-free delight?
Step‑by‑Step Instructions for Healthy Sourdough Discard Kolaches
Step 1: Prepare the Dough
In a stand mixer, combine 3 cups of einkorn flour, 1 cup of spelt flour, and 1 teaspoon of salt, ensuring a thorough mix. In a separate bowl, whisk together 1 cup of whole milk, ½ cup of melted butter, ¼ cup of sugar, 1 egg, 1 egg yolk, and 1 cup of sourdough starter until smooth. Gradually pour the wet mixture into the dry ingredients while mixing on low speed until a shaggy dough forms.
Step 2: Knead and Rise
Transfer the shaggy dough onto a lightly floured surface and knead it for about 8 to 10 minutes until smooth and elastic. The dough should feel slightly sticky but well-formed. Place the kneaded dough into a greased bowl, cover it with a damp cloth, and let it rise at room temperature for 1 hour. After it has puffed up noticeably, refrigerate overnight to deepen the flavor.
Step 3: Make the Filling
While the dough is chilling, prepare the creamy filling by beating together 8 ounces of softened cream cheese, ¼ cup of sugar, 2 tablespoons of all-purpose flour, 1 teaspoon of vanilla extract, and a pinch of salt in a mixing bowl. Aim for a smooth texture free of lumps. Chill the filling in the refrigerator until you’re ready to fill the kolaches for your Healthy Sourdough Discard Kolaches.
Step 4: Prepare Streusel
In another bowl, prepare the streusel by combining ½ cup of all-purpose flour, ¼ cup of sugar, and ¼ cup of softened butter. Mix these ingredients together with your fingertips until the mixture resembles sandy crumbs. Once ready, cover and chill the streusel until needed, ensuring a delightful topping for your kolaches.
Step 5: Shape the Dough
After the dough has risen overnight, punch it down gently to release air bubbles and transfer it onto a lightly floured surface. Cut the dough into 12 equal pieces and shape each piece into a smooth ball. Place the dough balls on a parchment-lined baking sheet, cover them with a cloth, and allow them to rise for 2 to 3 hours until puffy and slightly enlarged.
Step 6: Fill and Bake
Preheat your oven to 350°F (175°C). Once the dough balls have risen, create deep indentations in each ball using your thumb or fingers, being careful not to tear the dough. Fill each well generously with the chilled cream cheese mixture, then sprinkle the prepared streusel topping over each filled kolach. Brush the tops lightly with an egg wash (1 beaten egg) for a golden finish and bake for 20 to 25 minutes until the kolaches turn golden brown.
Step 7: Cool and Serve
After baked, remove the Healthy Sourdough Discard Kolaches from the oven and allow them to cool on the baking sheet for about 10 minutes. Then, transfer them to a wire rack to cool for an additional 20 minutes. Serve warm and enjoy the delightful contrast of creamy filling and tender pastry!

Make Ahead Options
These Healthy Sourdough Discard Kolaches are perfect for meal prep! You can prepare the dough up to 24 hours in advance by kneading and allowing it to rise for 1 hour at room temperature, then refrigerating overnight to enhance flavor. Additionally, the cream cheese filling can be mixed and stored in the refrigerator for up to 3 days, ensuring it stays fresh and ready to use. To maintain quality, cover the dough and filling tightly with plastic wrap. When you’re ready to bake, simply shape the dough, let it rise for 2 to 3 hours, fill with the chilled cream cheese, and bake as instructed for delightful, effortlessly prepared kolaches!
How to Store and Freeze Healthy Sourdough Discard Kolaches
Room Temperature: Keep kolaches in an airtight container at room temperature for up to 2 days for optimal freshness.
Fridge: To extend freshness, refrigerate kolaches in a sealed container for up to 4 days. Reheat in the oven for a few minutes to regain their delightful texture.
Freezer: Freeze kolaches in layers separated by parchment paper for up to 3 months. Thaw overnight in the fridge, then warm gently before serving.
Reheating: For best results, reheat thawed kolaches in the oven at 350°F (175°C) for 5–10 minutes to bring them back to life. Enjoy your Healthy Sourdough Discard Kolaches warm and delicious!
Healthy Sourdough Discard Kolaches Variations
Feel free to play around with this recipe and create your own delightful versions of kolaches that suit your taste and dietary needs!
- Cottage Cheese: Swap cream cheese for cottage cheese for a lighter, protein-packed filling. It’s a tangy alternative that offers a lovely texture.
- Fruit Preserves: Use your favorite fruit preserves instead of cream cheese for a sweet and fruity twist. Raspberry or apricot work beautifully!
- Gluten-Free: Substitute einkorn and spelt flour with a gluten-free flour blend to accommodate dietary restrictions without sacrificing flavor.
- Flavor Boost: Add a teaspoon of vanilla extract to the cream cheese filling for an aromatic enhancement. This extra layer of flavor makes all the difference!
- Chocolate Delight: Mix in some mini chocolate chips in the cream cheese filling for an indulgent dessert version that chocolate lovers will adore.
- Herbed Touch: Fold fresh herbs like chives or dill into the cream cheese filling for a savory spin that pairs perfectly with brunch!
- Spiced Filling: Stir in a pinch of cinnamon or nutmeg to the cream cheese for a warm, comforting essence. Perfect for cozy mornings!
- Nutty Crunch: Incorporate chopped nuts like pecans or walnuts into the filling or streusel topping for added texture and a delightful crunch.
As you experiment with these variations, you may also want to try serving your kolaches with fresh fruit, like berries or sliced peaches, alongside a cup of coffee or a refreshing tea for a complete breakfast experience. And if you’re ever in the mood for more nutritious indulgences, check out my Chunky Monkey Overnight for a delightful twist on oats, or whip up some Pumpkin Protein Balls for a snack that packs a nutritional punch!
Expert Tips for Healthy Sourdough Discard Kolaches
- Don’t Over-Flour: Ensure your dough remains slightly sticky; too much flour can result in dense kolaches.
- Rise Time Matters: Allow your dough ample rising time until it’s noticeably puffed for light and airy pastries.
- Room Temperature Cream Cheese: Use softened cream cheese for a smoother filling that blends beautifully without lumps.
- Create Deep Indentations: Make sure to create deep wells in the dough before filling; this will prevent spills during baking.
- Storage Tips: In warm climates, refrigerate your dough to keep it fresh, extending the life of your delicious Healthy Sourdough Discard Kolaches.
What to Serve with Healthy Sourdough Discard Kolaches
These delightful pastries create a perfect backdrop for a comforting meal filled with delicious harmony.
- Fresh Fruit Salad: Bright, juicy berries and sweet peaches complement the tangy cream cheese filling, adding a refreshing touch.
- Savory Scrambled Eggs: Fluffy, well-seasoned scrambled eggs provide a hearty balance to the sweet kolaches, perfect for brunch gatherings.
- Herbal Tea: A warm, fragrant cup of chamomile or mint tea brings out the kolaches’ richness while offering relaxation.
- Greek Yogurt Parfaits: Layer creamy yogurt with honey and granola for a satisfying, wholesome pairing that echoes the kolaches’ textures.
- Honey Drizzle: A light drizzle of honey enhances the sweetness, providing an extra layer of flavor that you won’t be able to resist.
- Coffee: A bold cup of your favorite brew pairs perfectly with the kolaches, enhancing both flavors for a cozy start to your day.
- Cinnamon Sugar Dusting: A sprinkle of cinnamon sugar can elevate your kolaches to a new level of indulgence, making bites even more delightful.
- Nutty Granola: Sprinkle some granola for added crunch and nutty flavor that contrasts beautifully with the soft kolaches.
- Whipped Cream: A dollop of whipped cream on the side adds a luxurious touch, making each bite melt in your mouth.
- Dark Chocolate Drizzle: For a touch of decadence, drizzle melted dark chocolate over the top, turning these pastries into an indulgent dessert.

Healthy Sourdough Discard Kolaches Recipe FAQs
How do I select the right sourdough starter for making kolaches?
Absolutely! When choosing your sourdough starter, look for one that’s active and bubbly. A healthy starter will provide the best rise and tanginess to your kolaches. If yours has been sitting for a while, give it a feeding 4 to 6 hours before baking to ensure it’s bubbly and fully active!
What is the best way to store Healthy Sourdough Discard Kolaches?
For those delectable kolaches, the best approach is to keep them in an airtight container at room temperature for up to 2 days. If you want a bit more longevity, go ahead and refrigerate them in a sealed container for up to 4 days. Just remember to warm them up in the oven for about 5 minutes before serving to bring back that fresh-baked taste!
Can I freeze Healthy Sourdough Discard Kolaches?
Yes! If you have extra kolaches, freeze them in layers separated by parchment paper for up to 3 months. To thaw, place them in the fridge overnight. Once thawed, reheat them in the oven at 350°F (175°C) for 5–10 minutes to regain their delightful texture and enjoy them warm!
My dough is too sticky; what should I do?
Very understandable! If your dough feels overly sticky, it might be best to add just a tablespoon of flour at a time during kneading until it reaches the right consistency. Remember, it’s okay for the dough to be slightly sticky; it usually makes for a lighter final product. Just be careful not to add too much flour, as this can lead to denser kolaches.
Can I make variations of the filling?
Absolutely! Think outside the box! Instead of cream cheese, you could fill your kolaches with cottage cheese or even fruit preserves for a unique twist. Just keep an eye on the consistency of the filling to maintain that creamy texture that contrasts perfectly with the dough!
Are Healthy Sourdough Discard Kolaches safe for my pets?
It’s best to keep these kolaches away from pets, especially since they contain butter, sugar, and cream cheese. While a tiny taste might not cause harm, the richness and sweetness are not suitable for pets, so it’s best to indulge yourself and keep these delicious treats for your own enjoyment!

Healthy Sourdough Discard Kolaches for a Guilt-Free Indulgence
Ingredients
Equipment
Method
- Prepare the Dough: In a stand mixer, combine 3 cups of einkorn flour, 1 cup of spelt flour, and 1 teaspoon of salt. In a bowl, whisk together milk, melted butter, sugar, egg, egg yolk, and sourdough starter. Gradually pour wet mixture into dry ingredients while mixing until a shaggy dough forms.
- Knead and Rise: Transfer dough to a floured surface and knead for 8 to 10 minutes. Place in greased bowl, cover, and let rise for 1 hour, then refrigerate overnight.
- Make the Filling: Beat together cream cheese, sugar, flour, vanilla extract, and salt until smooth. Chill in the refrigerator until ready.
- Prepare Streusel: Combine flour, sugar, and softened butter. Mix until sandy crumbs form, then chill.
- Shape the Dough: After refrigerating, punch down dough, cut into 12 pieces, shape into balls, and let rise for 2 to 3 hours.
- Fill and Bake: Preheat oven to 350°F. Create indentations in dough balls, fill with cream cheese mixture, sprinkle streusel topping, brush with egg wash, and bake for 20 to 25 minutes.
- Cool and Serve: Allow to cool for 10 minutes on baking sheet, then transfer to wire rack to cool for an additional 20 minutes.

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