Sourdough Apple Zucchini Muffins
These soft and moist sourdough apple zucchini muffins are made with freshly shredded apples, zucchini, sourdough discard, and a little cinnamon. They're lightly sweetened with honey and brown sugar and make a delicious breakfast or afternoon snack. Plus, they're freezer-friendly, so you can make a batch now and enjoy them later!

This apple zucchini muffins recipe is a glow-up from my grandma's original zucchini muffin recipe. In fact, you'll see version of it repeated over and over again throughout my blog!
The original recipe is Sourdough Banana Bread, followed by Banana Zucchini Bread, Peach Zucchini Bread, Banana Zucchini Muffins and I just keep adding more and more!
The cool thing about baking is once you find a perfect recipe that's a huge hit with your family, oftentimes you can create your own delicious recipe spinoff just by making a few ingredient swaps! For more variations, see my tips towards the bottom of this post.
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Why You'll Love This Recipe
- The natural sweetness of the apple mixture will make these healthy zucchini muffins your new favorite!
- Great way to use up extra sourdough discard!
- Beginner friendly sourdough recipe!
- Healthy snack! Freeze the leftovers for later.
Tips for Perfect Muffins
- Measure carefully.
- Stir until just combined.
- Prep the pan with parchment liners or cooking spray.
- Poke your muffin with a toothpick. If it comes out clean or with just a few crumbs, it's done!
- Let your muffins chill out in the pan for 10 minutes before transferring to a cooling rack.
Helpful Equipment
- two 12-cup muffin tin pans - this recipe makes 18 standard muffins or 36 mini muffins
- measuring spoons & cups
- parchment paper muffin liners and cooking spray
- stand mixer & spatula

Ingredients
Wet Ingredients
- Apples (300 grams) - Use any apple! I prefer fuji, gala, honey crisp or granny smith for this recipe. Use a cheese grater, food processor or kitchen aid mixer attachment to shred the apples. Leave the skin on, but remove the stems, cores and seeds. The amount of apples needed will depend on the size of your apples, but I've been using 3 large apples and it's been perfect.
- Zucchini (100 grams) - I either shred my zucchini with a box grater or use the shredder attachment on my kitchen aide mixer. Let the shredded zucchini sit in a strainer or on folded paper towels for 10 minutes to allow the moisture to drain before adding to batter. See my tip below for saving extra shredded zucchini for next time!
- Eggs & butter - set them out 20 minutes prior to baking to give them time to come to room temperature. Using melted butter instead of softened butter can result in a denser, flatter muffin.
- Honey - or substitute maple syrup
- Sourdough starter discard - 1 cup sourdough starter active or discard
- Vanilla extract - if you love high quality vanilla extract but can't afford the high price tag, make your own! Here's my Homemade Bourbon Vanilla tutorial.
- Brown sugar
Dry Ingredients
- All purpose flour - You can substitute whole wheat flour, see my tip below for detailed instructions.  If  using fresh milled flour, you will mill about 1 ⅓ cups of wheat berries to achieve 2 cups of all purpose flour. Sifting is recommended, but not necessary.
- Baking soda
- Salt & Cinnamon



Instructions
- Preheat oven to 350℉ and prepare two muffin pans with parchment liners and cooking spray.
- Whisk together dry ingredients in a medium bowl and set aside.
- In a separate bowl or stand mixer, beat room temperature butter and brown sugar two minutes until light and fluffy.
- Add in eggs, beating well after each addition.
- Add honey, vanilla, and sourdough starter.
- Slowly fold in the dry ingredients and plus shredded zucchini and apple and mix the muffin batter until just combined.
- Use an ice cream scoop to fill the muffin cups ⅔ full. Bake for about 22 minutes, or until the internal temperature at the center of the center muffin reaches 200°F with a thermometer.
- Leave the muffins in the muffin pan for 10-15 minutes before inverting it onto a wire rack to cool. This gives the muffins a chance to set slightly, preventing it from falling apart when you invert it.

Variations
- For a richer flavor, use brown butter.
- Use a dark brown sugar for a deeper molasses flavor.
- Stir in 1 cup of pecans and sprinkle crushed pecans over the top of the muffins for a heartier breakfast!
Substitutions
- Apples: You can omit the zucchini and use 4 apples to make this recipe.
- Zucchini: You can substitute 100 grams of shredded carrots for the grated zucchini.
- Sweetener: For a white sugar free option, use granulated monk fruit sweetener in a 1:1 ratio.
- Butter: You can substitute the butter with equal parts vegetable oil, canola oil or melted coconut oil. I do not recommend subbing olive oil for butter.

Storage
- Room temperature: For optimal freshness and flavor, store your delicious muffins in an airtight container at room temperature for up to 3 days.
- Freezing:For longer storage, wrap the cooled muffins tightly in plastic wrap or aluminum foil, then place it in a freezer bag. Freeze for up to 3 months. To thaw, let it sit on the counter overnight.
Tip: A baked muffin is very moist, so I recommend using cupcake liners for easier handling. Plain parchment liners are one of my favorite things for baking these healthy muffins!
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Converting Standard Muffins to Mini Muffins
A standard muffin recipe that makes 18 muffins will typically yield about 36–48 mini muffins, depending on the size of your muffin pan and how full you fill each cup.
Adjusting Baking Time
- Keep the oven temperature the same as the original recipe.
- Start checking for doneness at 10–12 minutes. Mini muffins generally take about 10–15 minutes to bake, depending on their size.
- Check for doneness by inserting a toothpick into the center of a muffin. It should come out clean or with a few moist crumbs, but no wet batter.
Mini muffins bake much faster than standard muffins, so keep an eye on them during the last few minutes to avoid overbaking.
FAQ
Yes. Whole wheat flour will make the batter a little more dense. To compensate for this, add a little more moisture to the muffin dough, such as an extra egg or some milk. You can also reduce the baking time slightly, as whole wheat flour tends to cook a bit faster than all-purpose flour.
Absolutely! To freeze zucchini, grate it, then squeeze out excess moisture. Place in freezer-safe bags and freeze for up to 3 months. Thaw completely before using in your recipe.
For short-term storage, keep the muffins in an airtight container at room temperature for up to 3 days. For longer storage, freeze the muffins in a container or Ziploc freezer bag. Muffins can be frozen for up to 3 months.
Most Popular Quick Breads
Guess what? This easy muffin recipe is also my favorite Banana Zucchini Bread recipe! I can't decide which version is better!
Best Sourdough Banana Bread- as the name implies, this really is the best banana bread recipe. Truly it's my favorite quick bread. And as a bonus, it's sourdough! A chocolaty version of my basic banana bread recipe are these Sourdough Discard Chocolate Banana Bread Bars and Fudgy Sourdough Banana Bread.
If you are looking for a good quick bread for a nice brunch or party, you should try Lemon Blueberry Cheesecake Bread. It tastes as beautiful as it looks! If you are more of a cranberry fan, here's the Cream Cheese Cranberry Bread version!
New on the Homestead
Recipe

Sourdough Apple Zucchini Muffins
Equipment
- large mixing bowl or stand mixer
- Muffin pans (makes 18 muffins)
- measuring cups & spoons
- Parchment paper muffin liners and cooking spray
Ingredients
Wet ingredients
- 300 grams apples stem and core removed, shredded (*see note below)
- 100 grams zucchini shredded
- 2 eggs large, room temperature
- â…“ cup honey or maple syrup
- 1 cup sourdough starter discard or active
- 8 tablespoons butter room temperature
- ¼ cup brown sugar packed
- 1 teaspoon vanilla
Dry ingredients
- 2 cups all-Purpose flour
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 teaspoon cinnamon
Instructions
- Preheat oven to 350℉ and prepare two muffin pans with parchment liners and cooking spray.
- Prepare apples by removing core, seeds and stem. Leave the skin on. Shred with a box grater or food processor. A standard apple, cored and shredded, weighs 100 grams. This recipe requires 3 apples. Shred the zucchini and let it sit on a paper towel or in a strainer for 10 minutes to release moisture before adding to recipe.
- Whisk together dry ingredients in a large mixing bowl and set aside.
- In a separate bowl or stand mixer, beat room temperature butter and brown sugar two minutes until light and fluffy.
- Â Add in eggs, beating well after each addition.
- Add honey, vanilla, sourdough starter and stir well.
- Slowly fold in the dry ingredients, apples and zucchini. Mix the muffin batter until just combined.
- Fill the muffin cups ⅔ full. Bake for about 22 minutes, or until the internal temperature at the center of the center muffin reaches 200°F with a thermometer.
- Â Leave the muffins in the muffin pan for 10-15 minutes before inverting it onto a wire rack to cool. This gives the muffins a chance to set slightly, preventing it from falling apart when you invert it.Â
Notes
- Apples: You can omit the zucchini and use 4 apples to make this recipe.
- Zucchini: You can substitute 100 grams of shredded carrots for the grated zucchini.
- Sweetener: For a white sugar free option, use granulated monk fruit sweetener in a 1:1 ratio.
- Butter: You can substitute the butter with equal parts vegetable oil, canola oil, melted coconut oil, or applesauce.Â










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