Before prepackaged muffins and mixes, simple homemade apple carrot muffins were a farmhouse favorite. These muffins were a wholesome way to use what was on hand. Grated apple adds natural sweetness and moisture, while fresh carrots bring a subtle earthiness and color that make each bite feel comforting. These are the kind of muffins that taste even better the next morning, enjoyed with a bit of butter and hot coffee at the kitchen table.

Apple carrot sourdough discard muffins baked and ready to serve for an old-fashioned breakfast.

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Apple carrot sourdough discard breakfast muffins baked until golden and arranged on a marble surface.

If you enjoy old-fashioned flavors, you may also like my Sourdough Discard Apple Cinnamon Muffins, or for a lighter, more nourishing breakfast, my Healthy Sourdough Morning Glory Muffins with Fresh Milled Wheat. Both are made with the same slow, simple approach to baking that makes this recipe one you’ll come back to.

Quick Look at This Recipe

Prep Time:
15 minutes
Bake Time:
18–22 minutes
Total Time:
About 35 minutes
Yield:
12 muffins
Flour Used:
All-purpose flour with a fresh milled wheat substitution option
Sourdough:
Uses sourdough starter discard for flavor and moisture
Texture:
Moist and tender with grated apple and carrot throughout
Best For:
Breakfast muffins, sourdough discard baking, or make-ahead snacks

Ingredients

Dry Ingredients

1 ¾ cups (250 g) all-purpose flour (or see substitution below for fresh milled flour)

1 teaspoon (4 g) baking powder

½ teaspoon (1.25 g) baking soda

½ teaspoon (1.5 g) salt

1 teaspoon (2.6 g) cinnamon

Wet Ingredients

½ cup (120g) sourdough discard

2 large eggs (100 g), room temperature

½ cup (110 g) light brown sugar

⅓ cup (67 g) granulated sugar

½ cup (113 g) melted butter or coconut oil, cooled slightly

1 teaspoon (5 g) vanilla extract

1 ½ cups (165 g) finely grated carrots (about 2 medium carrots)

1 large grated apple (about 1 cup / 125 g, peeled or unpeeled)

Instructions

Dry ingredients including flour and spices combined in a glass bowl for apple carrot muffins.

Preheat oven to 350°F (177°C). Line a muffin tin with paper liners or grease lightly. In a large bowl, whisk together flour, baking powder, baking soda, cinnamon, and salt until evenly combined.

Wet ingredients mixed together in a bowl before combining with dry ingredients for sourdough muffins.

In another bowl, whisk the eggs, sourdough discard, brown sugar, granulated sugar, melted butter, and vanilla extract until smooth and slightly thickened.

Adding flour mixture to the wet ingredients while making apple carrot sourdough discard muffin batter

Pour the wet ingredients into the dry and stir gently until just combined, don’t overmix! The batter should look thick but moist.

Apple carrot sourdough discard muffin batter partially mixed in a glass bowl with a spatula.

Fold in the grated carrots and grated apple.

Sourdough discard muffin batter portioned into a silicone muffin pan before baking.

Scoop the batter evenly into 12 muffin cups. Bake for about 18–22 minutes, or until a toothpick inserted in the center comes out clean and the tops are golden brown.

Freshly baked apple carrot sourdough discard muffins cooling in a silicone muffin pan on a baking sheet.

Let muffins cool in the pan for 5 minutes before transferring to a wire rack. Serve warm or at room temperature with butter, honey, or your favorite spread.

Close up of an apple carrot sourdough discard muffin showing a soft, tender crumb.

Using Freshly Milled Wheat Flour (Soft White) for Apple Carrot Sourdough Discard Muffins

If you prefer baking the old-fashioned way, as I do, you can swap the all-purpose flour for freshly milled soft white wheat flour. Soft milled wheat flour can be used in this recipe at a 1:1 ratio by weight in place of all-purpose flour. Because freshly milled flour absorbs moisture differently, it helps to hold back 1 to 2 tablespoons of the flour at first.

After mixing, let the batter rest for about 10 minutes so the bran has time to hydrate, then adjust if needed. This keeps the muffins moist while balancing the moisture from the apple, carrot, and sourdough discard. Soft milled wheat also offers the most nutrition when used soon after milling, along with a mild, slightly sweet flavor that works well in old-fashioned breakfast muffins.

Tips & Variations

Add a handful of chopped walnuts or raisins for a bit of texture.
Swap butter for coconut oil to make them dairy-free.
These freeze beautifully, just wrap individually and store in an airtight bag.

Apple carrot sourdough discard muffins freshly baked and ready to enjoy as an old-fashioned breakfast.

Frequently Asked Questions About Old-Fashioned Sourdough Discard Apple Carrot Muffins

Can I make these muffins ahead of time?

Yes! They keep well at room temperature for 2 days or refrigerated for up to 5.

Do these taste like carrot cake?

A little — but they’re lighter, less sweet, and made for breakfast rather than dessert.

Can I make these apple carrot muffins without sourdough discard?

Sourdough discard adds flavor and moisture, but if you do not have any on hand, you can substitute plain yogurt or applesauce in a pinch. The texture will be slightly different, but the muffins will still bake up soft and flavorful.

Do I need to peel the apple and carrot first?

Peeling is recommended for the smoothest texture, especially for breakfast muffins. Leaving the peels on is fine if you prefer a heartier, more rustic feel.

Can I use fresh milled wheat instead of all-purpose flour?

Yes! Fresh milled wheat works beautifully in these muffins and it's the way that we prefer to have them. Because it absorbs moisture differently, allow the batter to rest briefly before baking so the flour can fully hydrate.

How should I store apple carrot sourdough discard muffins?

Store the muffins in an airtight container at room temperature for up to two days or in the refrigerator for up to five days. They also freeze well for longer storage.

What other recipes use carrots and sourdough starter?

If you enjoy the apple and carrot combination, you may also like my Sourdough Carrot Cake with Cream Cheese Frosting, which uses sourdough starter to add depth and richness to a classic dessert.

Single apple carrot sourdough discard muffin served on a plate for breakfast.

Bring the Joy of Homemade Baking

These apple carrot muffins are everything we love about simple, old-fashioned baking, made with real ingredients and a touch of nostalgia. Whether you bake them for a cozy breakfast or pack them in lunchboxes, they’re the kind of recipe you’ll come back to again and again.

Tried this recipe?

I would love to see it! Tag me on Instagram @idiesfarm and #idiesfarm so I can share your beautiful creation!