• Skip to main content
  • Skip to primary sidebar
Simple And Fraiche
menu icon
go to homepage
  • Thanksgiving
  • Smoking And Grilling
  • Recipe Index
  • About
  • Work With Me
    • Amazon
    • Instagram
    • Pinterest
  • search icon
    Homepage link
    • Thanksgiving
    • Smoking And Grilling
    • Recipe Index
    • About
    • Work With Me
    • Amazon
    • Instagram
    • Pinterest
  • ×
    Home » Recipes » Sourdough

    Sourdough Apple Muffins Recipe

    Published: Feb 7, 2025 by Nadia · This post may contain affiliate links · 1 Comment

    56 shares
    • Facebook
    • X
    • Flipboard
    • Email
    • LinkedIn
    Jump to Recipe Print Recipe

    This easy and delicious Sourdough Apple Muffins recipe will make your kitchen smell amazing! These muffins are soft, perfectly spiced, and a great way to use up sourdough discard. They're packed with fresh apples and warm cinnamon, and ready in just 30 minutes.

    Sourdough apple muffins with brown tops sit in a baking pan lined with parchment paper. Beside them, theres an apple cut into cubes and a muffin split open, revealing a moist interior. Cinnamon sticks and a whole apple are in the background.

    Tired of tossing your sourdough discard but don't want to deal with another loaf of sourdough bread? I get it-wasting starter feels wrong, and that's where these sourdough apple cinnamon muffins come in!

    As someone who's pretty obsessed with wholesome ingredients, I've perfected a foolproof recipe that turns your extra discard into light, fluffy muffins bursting with fresh apples and warm cinnamon-no long fermentation, no fuss.

    Just mix, bake, and enjoy a bakery-worthy treat that proves sourdough can do so much more than just bread!

    If you are looking for more easy sourdough recipes check out my Mixed Berry Galette With Sourdough Crust, Sourdough Chocolate Chip Cookies, Sourdough Pound Cake, Sourdough Pumpkin Muffins, or Sourdough Brownies. You may also enjoy my Cottage Cheese Blueberry Muffins or Banana Cottage Cheese Muffins.

    Jump to:
    • Why You'll Love This Recipe
    • Ingredients
    • Substitutions And Variations
    • How To Make Apple Sourdough Muffins
    • Expert Tips And Notes
    • Serving Suggestions For Sourdough Discard Apple Muffins
    • Storage And Reheating
    • Recipe FAQs
    • Other Related Sourdough Discard Recipes
    • Sourdough Apple Muffins Recipe

    Why You'll Love This Recipe

    • No Waste And Great Taste: This recipe is a great way to use up your extra sourdough discard. The sourdough also helps to create a light and fluffy texture.
    • Easy To Make: You only need a handful of simple ingredients, and there are no complicated steps required!
    • Incredible Flavor: Packed with tons of fresh apples and warming spices, these sourdough apple muffins are a delightful treat.

    Ingredients

    A collection of baking ingredients on a white surface: almond flour, gluten-free flour, butter, coconut sugar, eggs, cottage cheese, sourdough discard, apples, vanilla, cinnamon, sea salt, baking soda, nutmeg, and cloves.
    • Unsalted Butter: You will want to use unsalted organic grass-fed butter. Make sure it is room temperature, which will allow it to mix easily with the sugar.
    • Coconut Sugar: I love using coconut sugar since it's unrefined. If you don't have coconut sugar, date sugar would be a good swap. 
    • Eggs: When shopping for eggs, look for organic pasture-raised eggs. For this recipe, you will want to let these eggs come up to room temperature beforehand. This will help them mix into the batter smoothly.
    • Sourdough Discard: There is no need to use an active sourdough starter! Just grab your sourdough discard from the fridge and add it in! It will add lightness and fluffiness to the muffins.
    • Cottage Cheese: I love baking with cottage cheese. I recommend using Good Cultures's full-fat or low-fat cottage cheese. It may seem like a surprising ingredient to find in a sourdough muffin recipe, but I promise it adds a lot of moisture, along with some extra protein-and I promise you won't even taste it!
    • Vanilla Bean Paste: More concentrated and flavorful than vanilla extract, enhancing the muffins with a deep, rich vanilla taste. If you don't have vanilla bean paste, you can totally use vanilla extract.
    • Gluten-Free Flour And Almond Flour: I love using a mix of gluten-free flour and almond flour. The almond flour adds extra softness and chewiness. If you are not gluten-free, feel free to use regular all-purpose flour.
    • Sea Salt: Sea Salt helps to balance sweetness and enhance the other flavors. You can also use kosher salt, but avoid table salt.
    • Baking Soda: This will help your muffins rise. We are using baking soda not baking powder in this recipe!
    • Cinnamon, Nutmeg, And Cloves: This is one of my favorite cozy spice combos! It brings a ton of warmth and depth to the muffins. You could use apple pie spice instead if you have it.
    • Apples: Feel free to use any crisp apples you like, but I highly recommend using pink lady apples or Honey crisp as they both are slightly tart and sweet.

    See the recipe card for full information on ingredients and quantities.

    Substitutions And Variations

    • Apples: While I prefer using pink lady or honey crisp, feel free to use granny smith apples or swap the apples entirely for pears.
    • Mix-Ins: Experiment by adding chopped walnuts, pecans, or raisins.
    • Dairy-Free: Swap the butter for melted coconut oil to make this recipe dairy-free.

    How To Make Apple Sourdough Muffins

    This is an overview with step-by-step photos. Full ingredients & instructions are in the recipe card below.

    A top view of a muffin tin with twelve individual slots, each lined with a brown parchment paper liner. The liners are shaped like tulip cups, ready for batter. The muffin tin is placed on a white surface.

    Step 1. Preheat your oven to 350 degrees. Line your muffin pan with individual parchment paper liners.

    A metal spoon is partially buried in a mound of white flour in a clear glass bowl, placed on a white marble surface.

    Step 2. Add the gluten-free flour, almond flour, sea salt, baking soda, cinnamon, nutmeg, and cloves to a medium bowl and whisk to combine.

    A mound of coconut sugar and a stick of butter in a metallic mixing bowl. The edge of a mixer paddle is visible above them.

    Step 3. Add the butter and sugar to the bowl of a stand mixer and use the paddle attachment to mix until light and fluffy.

    Sourdough Apple Muffin batter mix in a metal stand mixer bowl.

    Step 4. Add the eggs, sourdough discard, cottage cheese, and vanilla bean paste, and mix again until combined.

    A bowl filled with sourdough apple muffin batter.

    Step 5. Gradually add the flour mixture to the wet ingredients and mix until just combined.

    Sourdough apple muffin batter.

    Step 6. Use a spatula or wooden spoon to gently fold in the diced apples.

    Save This Recipe! 📧

    We'll email this post to you, so you can come back to it later!

    Overhead view of  apple sourdough muffin batter with chunks of apple in brown paper liners arranged in a muffin tin, ready to be baked.

    Step 7. Use a cookie scoop to scoop the muffin batter into the muffin cups. You will want to fill them about ¾ of the way full. Add a pinch of coconut sugar or turbinado sugar to the top of the muffins for a little crunch. Bake for 15-20 minutes, until cooked through and golden brown.

    Expert Tips And Notes

    • Don't Overmix: For best results stir the batter until the wet and dry ingredients are just combined-there should still be a few streaks of flour visible before folding in the apples.
    • Use Sweet And Tart Apples: Honey crisp and Pink Lady or Pink Crisp apples are great choices because they hold their shape and add a nice balance of sweetness and tartness.
    • Use Muffin Liners: Don't underestimate the power of muffin liners! Parchment paper liners make cleanup a breeze and give your muffins a polished, bakery-style look.

    Serving Suggestions For Sourdough Discard Apple Muffins

    • Toppings: Slather with creamy almond butter for a nutty boost, or drizzle with honey or smoked butter.
    • Breakfast Pairings: Enjoy with a side of cottage cheese and fruit for a protein-packed start to the day, or serve alongside high-protein egg bites and smoked bacon for a well-rounded meal.
    • Additional Desserts: Warm up the muffins and serve with a scoop of cinnamon or vanilla ice cream for a cozy fall-inspired treat, or top with a dollop of maple whipped cream for extra indulgence.
    • Beverages: These muffins are perfect with an iced maple latte, a classic cappuccino, or a pumpkin spiced latte.

    Storage And Reheating

    • Storage: Store in an airtight container at room temperature for up to 3-4 days or in the refrigerator for up to 1 week.
    • Freezing: Wrap each muffin individually in plastic wrap and store in a freezer-safe bag for up to 3 months.
    • Reheating: Place in an oven-safe dish and reheat at 250 degrees for 3-5 minutes.

    Recipe FAQs

    Can I make these muffins without sourdough discard?

    Yes! Substitute the discard with Greek yogurt for a similar texture.

    How do I know when the muffins are done?

    Insert a toothpick into the center-if it comes out clean, they're ready!

    Why did my muffins turn out dense?

    Over-mixing the batter can cause dense muffins. Stir gently and stop once everything is just combined.

    A batch of freshly baked sourdough apple muffins with chunks of apple and cinnamon, each wrapped in parchment paper, arranged on a wooden table. Next to them is an apple and a small bowl containing cinnamon sticks.

    Other Related Sourdough Discard Recipes

    • Close-up of homemade bread stuffing with chunks of toasted bread, chopped celery, onions, and herbs, baked until golden and tender in a casserole dish.
      Easy Sourdough Bread Stuffing With Fresh Herbs
    • Close-up of sliced apple sourdough bread, topped with a light drizzle of icing. The bread is moist, filled with apple chunks, and rests on parchment paper.
      Apple Sourdough Bread (Moist + Easy Fall Recipe)
    • Pumpkin sourdough muffins in a muffin tin.
      Sourdough Pumpkin Muffins (Easy Discard Recipe)
    • Two clear glasses filled with layered strawberry shortcake, featuring diced strawberries, chunks of cake, and dollops of whipped cream. A fresh strawberry slice garnishes the top. A bowl of strawberries and a gold spoon are in the background.
      Easy Strawberry Shortcake Parfaits (With Pound Cake)

    If you tried this recipe please leave a 🌟 star rating and let me know how it went in the 📝 comments below. You can also stay in touch through social media by following along on Instagram, Pinterest, YouTube, or Facebook. Thanks for visiting today!

    Three apple sourdough muffins in paper liners sit in a baking tray next to chopped apple pieces in another compartment. A sliced muffin with apple chunks is on a plate nearby, alongside two cinnamon sticks and a whole apple.

    Sourdough Apple Muffins Recipe

    Nadia
    This easy and delicious Sourdough Apple Muffins recipe will have your kitchen smelling amazing! These muffins are soft, perfectly spiced, and a great way to use up sourdough discard. They're packed with fresh apples, warm cinnamon, and just the right amount of sweetness.
    5 from 2 votes
    Print Recipe Pin Recipe
    Prevent your screen from going dark
    Prep Time 10 minutes mins
    Cook Time 20 minutes mins
    Total Time 30 minutes mins
    Course Dessert
    Cuisine American
    Servings 12
    Calories 159 kcal

    Ingredients
      

    • 8 tablespoons Butter unsalted, room temperature
    • ¾ cup Coconut Sugar
    • 2 Eggs room temperature
    • ¾ cup Sourdough Discard
    • ½ cup Cottage Cheese
    • 1 tablespoon Vanilla Bean Paste
    • 1 cup Gluten-Free Flour
    • ½ cup Almond Flour
    • ½ teaspoon Sea Salt
    • 1 teaspoon Baking Soda
    • 1 teaspoon Cinnamon
    • ¼ teaspoon Nutmeg
    • ⅛ teaspoon Cloves
    • 2 Medium Apples diced
    Prevent your screen from going dark

    Instructions
     

    • Preheat your oven to 350 degrees. Line your muffin pan with individual parchment paper liners.
    • Add the gluten-free flour, almond flour, sea salt, baking soda, cinnamon, nutmeg, and cloves to a medium bowl and whisk to combine.
      1 cup Gluten-Free Flour, ½ cup Almond Flour, ½ teaspoon Sea Salt, 1 teaspoon Baking Soda, 1 teaspoon Cinnamon, ¼ teaspoon Nutmeg, ⅛ teaspoon Cloves
    • Next add the butter and sugar to the bowl of a stand mixer and use the paddle attachment to mix until light and fluffy.
      8 tablespoons Butter, ¾ cup Coconut Sugar
    • Add the eggs, sourdough discard, cottage cheese, and vanilla bean paste, and mix again until combined.
      2 Eggs, ¾ cup Sourdough Discard, ½ cup Cottage Cheese, 1 tablespoon Vanilla Bean Paste
    • Gradually add the flour mixture to the wet ingredients and mix until just combined.
    • Use a spatula or wooden spoon to gently fold in the diced apples.
      2 Medium Apples
    • Use a cookie scoop to scoop the muffin batter into the muffin cups. You will want to fill them about ¾ of the way full. Add a pinch of coconut sugar or turbinado sugar to the top of the muffins for a little crunch. Bake for 15-20 minutes, until cooked through and golden brown.

    Notes

    Expert Tips And Notes
    • Don't Over-mix: For best results stir the batter until the wet and dry ingredients are just combined-there should still be a few streaks of flour visible before folding in the apples.
    • Use Sweet And Tart Apples: Honey crisp and Pink Lady or Pink Crisp apples are great choices because they hold their shape and add a nice balance of sweetness and tartness.
    • Use Muffin Liners: Don't underestimate the power of muffin liners! Parchment paper liners make cleanup a breeze and give your muffins a polished, bakery-style look.

    Nutrition

    Calories: 159kcalCarbohydrates: 31gProtein: 3gFat: 3gSaturated Fat: 1gPolyunsaturated Fat: 0.1gMonounsaturated Fat: 0.2gTrans Fat: 0.02gCholesterol: 2mgSodium: 308mgPotassium: 47mgFiber: 2gSugar: 16gVitamin A: 30IUVitamin C: 1mgCalcium: 49mgIron: 1mg
    Tried this recipe?Let us know how it was!

    More Sourdough Recipes

    • Sliced sourdough pound cake on a parchment paper next to a bowl of fresh strawberries.
      The Best Sourdough Pound Cake Recipe
    • Sourdough Chicken Pot Pie in a cast iron. One slice is missing.
      Sourdough Chicken Pot Pie
    • Two bowls of sourdough chicken and dumplings soup with silver spoons sticking out of each bowl.
      Sourdough Chicken And Dumplings
    • Sourdough Starter Discard in a glass jar with a wooden spoon scooping it out.
      How Long Does Sourdough Discard Last?

    Subscribe

    for your weekly recipe fix.

    Reader Interactions

    Comments

    1. Nadia says

      February 07, 2025 at 9:34 pm

      5 stars
      I hope you love this recipe as much as we do! I had a blast creating it! One of my favorite ways to enjoy this muffin is with a cup of coffee as mid morning treat.

      Reply
    5 from 2 votes (1 rating without comment)

    Leave a Reply Cancel reply

    Your email address will not be published. Required fields are marked *

    Recipe Rating




    Primary Sidebar

    Nadia

    Hi, y'all! I’m Nadia the recipe creator, photographer, and writer behind Simple And Fraiche. I’m here to help you discover that cooking wholesome, nourishing meals can be approachable, enjoyable, and packed with flavor. 


    As someone with a background in health and fitness and a certified nutrition coach, I’ve worked with hundreds of clients who all face the same challenge: How can you eat foods that fuel your body and help you achieve your health goals without sacrificing flavor?

    My mission is to help you overcome that hurdle by sharing easy, nutrient-dense recipes that make you excited to get in the kitchen.

    More About Me

    Popular Recipes

    • Smashburger sauce in a white bowl with a gold spoon sticking out of it.
      Easy Smashburger Sauce Recipe
    • Turkish Labneh on a plate drizzled with olive oil and parsley.
      Turkish Labneh
    • Traeger Grilled Salmon on a sheet pan with asparagus, roasted potatoes and lemon.
      Traeger Grilled Salmon Recipe (With Garlic And Herbs)
    • Raw carrot salad in a black bowl topped with parsley.
      Raw Carrot Salad
    • Smoked hot dogs in a bun with toppings surrounding it.
      Smoked Hot Dogs On A Pellet Grill
    • Burst Cherry Tomato Pasta and Steak
      Burst Cherry Tomato Pasta With Steak

    Thanksgiving Favorites

    • A close-up of a bowl filled with thick, chunky homemade cranberry sauce, garnished with small bits of orange zest, with a spoon partially visible on the right side.
      Homemade Cranberry Sauce With Mandarin Oranges
    • A close-up of a whole roasted turkey with crispy, seasoned skin on a wooden board. A blurred orange and some fresh sage leaves are visible in the background.
      Juicy Traeger Smoked Turkey (Dry Brine Method)
    • A skillet filled with creamy smoked macaroni and cheese, garnished with fresh basil and a sprinkle of black pepper.
      Creamy Smoked Mac and Cheese (No Velveeta)
    • Roasted butternut squash and feta salad.
      Roasted Butternut Squash And Feta Salad (Easy Fall Recipe)
    • Slices of no-bake pumpkin cheesecake bars with a light brown color, each topped with a swirl of whipped cream and a sprinkle of cinnamon, on a brown parchment-lined surface.
      No Bake Pumpkin Cheesecake Bars (Easy Recipe)
    • Dutch Oven Braised Chicken thighs cooked with apple slices and herbs, including a sprig of rosemary and sage, in a light sauce. The dish is served in a white baking dish, highlighting the golden chicken and tender apples.
      Dutch Oven Braised Chicken Thighs (With Apple Cider)

    Footer

    ↑ back to top

    About

    • About
    • Privacy Policy

    Newsletter

    • Sign Up! for emails and updates

    Contact

    • Contact

    Copyright © 2025 Simple and Fraiche

    Rate This Recipe

    Your vote:




    Let us know what you thought of this recipe:

    This worked exactly as written, thanks!
    My family loved this!
    Thank you for sharing this recipe

    Or write in your own words:

    A rating is required
    A name is required
    An email is required

    Recipe Ratings without Comment

    Something went wrong. Please try again.