Whole Wheat Carrot Muffins are moist, flavorful, and filled with wholesome ingredients. With sweet carrots, warm spices, raisins, and pecans, they make a nutritious breakfast or snack you can feel good about.
Why You’ll Love This Recipe
- Made with whole wheat pastry flour for a light texture and extra nutrients.
- Naturally sweetened with applesauce and brown sugar.
- Packed with carrots, raisins, and nuts for flavor and texture.
- Perfect for meal prep and freezer-friendly.
- Great for a quick breakfast, lunchbox treat, or afternoon snack.

Ingredients
(Tip: You’ll find the full list of ingredients and measurements in the recipe card below.)
- 1 1/2 cups whole wheat pastry flour
- 1 teaspoon baking soda
- 3/4 teaspoon ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/2 teaspoon ground ginger
- 1/2 teaspoon salt
- 3/4 cup unsweetened applesauce
- 1/2 cup nonfat plain Greek yogurt
- 1/2 cup packed brown sugar
- 2 tablespoons canola oil
- 1 egg
- 1 cup lightly packed shredded carrots
- 1/3 cup golden raisins
- 1/3 cup chopped pecans
- 12 pecan halves (for topping)
Directions
- Preheat oven to 375°F. Lightly coat a muffin tin with cooking spray.
- In a medium bowl, whisk together flour, baking soda, cinnamon, nutmeg, ginger, and salt.
- In a large bowl, combine applesauce, Greek yogurt, brown sugar, canola oil, and egg. Stir until smooth.
- Gently fold dry ingredients into the wet mixture until combined.
- Stir in shredded carrots, raisins, and chopped pecans.
- Spoon batter evenly into muffin cups.
- Bake for 7 minutes, then place one pecan half on top of each muffin. Continue baking for an additional 7–9 minutes, or until a toothpick inserted in the center comes out clean.
- Remove muffins from the pan and cool before serving.
Servings and timing
- Servings: 12 muffins
- Prep time: 15 minutes
- Cook time: 14–16 minutes
- Total time: 29–31 minutes
Variations
- Swap golden raisins for dried cranberries or chopped dates.
- Use walnuts instead of pecans.
- Add shredded coconut for extra flavor.
- Replace some of the applesauce with mashed banana for a different sweetness profile.
- Sprinkle oats or coarse sugar on top for extra texture.
Storage/Reheating
- Store in an airtight container at room temperature for up to 3 days.
- Refrigerate for up to 5 days for longer freshness.
- Freeze for up to 2 months; thaw at room temperature or microwave for 20–30 seconds.

FAQs
Can I use regular whole wheat flour instead of pastry flour?
Yes, but the muffins may be denser. Pastry flour gives a lighter texture.
Can I make these muffins without nuts?
Yes, just omit the pecans or replace them with seeds like pumpkin or sunflower seeds.
Are these muffins very sweet?
They are mildly sweet; you can add more brown sugar if you prefer.
Can I make them gluten-free?
Yes, use a gluten-free all-purpose flour blend.
Can I use regular yogurt instead of Greek yogurt?
Yes, but Greek yogurt adds more protein and a thicker texture.
How do I keep muffins moist?
Don’t overbake, and store in an airtight container.
Can I double the recipe?
Yes, simply double the ingredients and bake in two muffin tins.
Can I make them vegan?
Yes, use plant-based yogurt and replace the egg with a flax egg.
Can I shred carrots ahead of time?
Yes, but store them in the fridge and pat dry before adding to batter.
Are these good for kids?
Yes, they’re a healthy and tasty snack for all ages.
Conclusion
Whole Wheat Carrot Muffins are a wholesome, flavorful treat that’s perfect for starting your day or enjoying as a snack. With their warm spices, natural sweetness, and tender texture, they strike the perfect balance between healthy and delicious — and they freeze beautifully for future grab-and-go mornings.
Print
Whole Wheat Carrot Muffin Recipe
- Total Time: 29–31 minutes
- Yield: 12 muffins
- Diet: Vegetarian
Description
Moist, lightly sweetened whole wheat carrot muffins made with applesauce, Greek yogurt, raisins, and pecans — a wholesome breakfast or snack that’s freezer-friendly.
Ingredients
1 1/2 cups whole wheat pastry flour
1 teaspoon baking soda
3/4 teaspoon ground cinnamon
1/2 teaspoon ground nutmeg
1/2 teaspoon ground ginger
1/2 teaspoon salt
3/4 cup unsweetened applesauce
1/2 cup nonfat plain Greek yogurt
1/2 cup packed brown sugar
2 tablespoons canola oil
1 egg
1 cup lightly packed shredded carrots
1/3 cup golden raisins
1/3 cup chopped pecans
12 pecan halves (for topping)
Instructions
- Preheat oven to 375°F. Lightly coat a muffin tin with cooking spray.
- In a medium bowl, whisk together flour, baking soda, cinnamon, nutmeg, ginger, and salt.
- In a large bowl, combine applesauce, Greek yogurt, brown sugar, canola oil, and egg. Stir until smooth.
- Gently fold dry ingredients into wet mixture until just combined.
- Stir in shredded carrots, raisins, and chopped pecans.
- Spoon batter evenly into muffin cups.
- Bake for 7 minutes, then place one pecan half on each muffin. Continue baking for an additional 7–9 minutes, or until a toothpick inserted in the center comes out clean.
- Remove from pan and cool before serving.
Notes
- Swap raisins for dried cranberries or chopped dates.
- Use walnuts instead of pecans for variation.
- Add shredded coconut for extra flavor.
- Replace some applesauce with mashed banana for a different taste.
- Top with oats or coarse sugar for added texture.
- Prep Time: 15 minutes
- Cook Time: 14–16 minutes
- Category: Breakfast
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 muffin
- Calories: 160
- Sugar: 10g
- Sodium: 200mg
- Fat: 7g
- Saturated Fat: 0.7g
- Unsaturated Fat: 5.5g
- Trans Fat: 0g
- Carbohydrates: 23g
- Fiber: 3g
- Protein: 4g
- Cholesterol: 15mg