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Wholemeal Apple and Carrot Muffins

These wholemeal apple and carrot muffins are a perfect way to start your day or to enjoy as a delicious afternoon snack. Packed with fresh grated apple, carrots, and whole grain flour, they’re a wholesome take on classic muffins without sacrificing flavor. Perfect for lunch boxes as they’re nut-free.

A muffin on a concrete bench next to two more muffins on a wooden cutting board. Moody light.
Table of contents

Why you’ll love the wholemeal muffins

  • Wholesome snack: Made with wholesome ingredients including dried and fresh fruit, carrots, and wholemeal flour, these tasty muffins make a delicious yet wholesome snack.
  • Moist and flavorful: Grated apple and carrot add natural sweetness and moisture, keeping these fall-inspired muffins delicious for days without the use of vegetable oil.
  • Great for meal prep: These delicious apple carrot muffins store well at room temperature or in the freezer for up to 3 months. They make the perfect on-the-go snack, easy breakfast on busy mornings, or nut-free school snack, just like my granola bars.

Ingredients & substitutions

Ingredients for apple and carrot muffins laid out on a wooden kitchen bench.
  • Carrots: Use 2 medium-sized carrots, peeled and grated, or one large carrot. Use a box grater or the shredding attachment on your food processor for quick and easy grating.
  • Apple: You’ll need 1 large grated apple (skin on). Choose a tart apple like Granny Smith for a nice balance of sweetness and sourness.
  • Brown sugar: Substitute with coconut sugar or granulated monk fruit sweetener in equal amounts for a refined sugar-free option).
  • Wholemeal flour: Substitute some or all with all-purpose flour for a fluffier texture.


  1. Morning glory muffins: Add 1/2 cup chopped walnuts to make classic morning glory muffins.
  2. Carrot cake muffins: Substitute the apple with more shredded carrot and add a cream cheese glaze.
  3. Streusel topping: Add a cinnamon streusel topping to your apple and carrot muffins for some indulgence and crunch.

How to make apple and carrot muffins

Steps 1-4 of how to make these muffins.
  1. Cream the butter and sugar and add the egg and whey (or milk). Mix until well combined.
  2. Mix all dry ingredients in a separate bowl.
  3. Grate the apple and carrots.
  4. Add the dry ingredients, grated apple and carrots, and raisins to the wet ingredients. Mix to combine but we careful not to overmix the muffin batter.


Can I freeze carrot apple muffins?

Yes, these moist muffins are great for meal prep. Store them in the freezer for up to 3 months in an airtight container or a plastic freezer bag.

Can I make these muffins gluten-free?

Yes, you can try using gluten-free flour our almond meal instead of wheat flour

For more delicious snack ideas, check out the following recipes:

If you loved this Apple and Carrot Muffin Recipe or any other recipe on my website, please leave a 🌟 star rating below. Thank you!

A muffin on a concrete bench next to two more muffins on a wooden cutting board. Moody light.

Wholemeal Apple and Carrot Muffins

Caro Jensen
Easy wholemeal apple and carrot muffins packed with wholesome ingredients – perfect for breakfast or as a nut-free lunchbox filler.
5 from 1 vote
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast, Dessert, Snack
Cuisine American
Servings 12 muffins
Calories 309 kcal


  • 1/2 cup butter softened
  • 3/4 cup brown sugar packed
  • 1 tsp vanilla extract
  • 2 eggs medium-sized
  • 3/4 cup whole milk
  • 2 cups wholemeal flour
  • 1 cup rolled oats
  • 2 tsp ground cinnamon
  • 1/2 cup raisins
  • 1 cup grated apple skin on
  • 1 cup grated carrots peeled, 2 medium-sized carrots


  • Preheat your oven to 400°F (200°C) and line a 12-cup muffin tin with paper liners (or coat with butter or nonstick spray).
  • In a large bowl, cream together the softened butter and brown sugar until light and fluffy. Beat in the eggs one at a time, then stir in the vanilla extract and milk.
    1/2 cup butter, 3/4 cup brown sugar, 1 tsp vanilla extract, 2 eggs, 3/4 cup whole milk
  • In a separate bowl, whisk together the wholemeal flour, oats, cinnamon, baking powder, and salt.
    2 cups wholemeal flour, 1 cup rolled oats, 2 tsp ground cinnamon
  • Gradually add the dry ingredients, grated carrots and apple, and raisins to the wet ingredients, mixing until just combined. Be careful not to overmix!
    1/2 cup raisins, 1 cup grated apple, 1 cup grated carrots
  • Divide the muffin batter evenly among the prepared muffin cups using an ice cream scoop for mess-free filling.
  • Bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Let the carrot apple muffins cool in the pan for a few minutes before transferring them from the muffin tray to a wire rack to cool completely.


Don’t overmix: Overmixing can lead to tough muffins. Once the dry ingredients are just incorporated, stop mixing.
Grate apple and carrots: Grating the apple and carrot ensures they are evenly distributed throughout the batter and bake evenly.
Double batch: Make a double or triple batch and freeze half once cooled for on-demand lunchbox fillers and snacks.


Calories: 309kcalCarbohydrates: 46gProtein: 6gFat: 12gSaturated Fat: 6gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.3gCholesterol: 49mgSodium: 336mgPotassium: 175mgFiber: 4gSugar: 18gVitamin A: 2089IUVitamin C: 1mgCalcium: 119mgIron: 2mg
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